@prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix InlineJavascriptRequirement: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix InplaceUpdateRequirement: . @prefix rdf: . @prefix Dirent: . @prefix cwl: . @prefix ResourceRequirement: . @prefix ExpressionTool: . rdfs:label "concat_logfiles_calib_cal" ; cwl:in , ; cwl:out ; cwl:run . sld:default "ant" . rdfs:label "BLsmooth" ; cwl:in , ; cwl:out , ; cwl:run . cwl:source . sld:default "bandpass" . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_image_name)" ] ; sld:type cwl:File . rdfs:label "concat_logfiles_blsmooth" ; cwl:in , ; cwl:out ; cwl:run . sld:default "DATA" . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; cwl:pickValue "all_non_null" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputimage)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "transfer_solutions" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "transfer_solutions.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parm)" ] ] ; cwl:stderr "transfer_solutions_err.log" ; cwl:stdout "transfer_solutions.log" . cwl:source ; sld:default "*" . rdfs:label "concat_logfiles_FR" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default true . a cwl:Workflow ; rdfs:label "predict_calibrate" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , , , , . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Rms to clip outliers, by default 5." ; sld:type xsd:float , sld:null . sld:default "plot_demix_solutions" . cwl:source . sld:default "apply_fr_bandpass" . rdfs:label "losoto_plot_Pr2" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "Solution interval in timesteps" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solint=" ; CommandLineBinding:separate false ] ; sld:default 1 ; sld:type xsd:int , sld:null . cwl:source ; sld:default "*" . cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default -3.14e+00 , 3.14e+00 . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:label "prep" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , ; cwl:run . rdfs:comment "If WEIGHT_SPECTRUM_ORIG exists then restore it before smoothing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-r" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-r" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "demix_solutions" ] ; sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "sol000/phase000" . cwl:source . rdfs:comment "Name of the h5parm from which the solutions should be transferred." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--refh5parm" ] ; sld:default "$LINC_DATA_ROOT/solutions/3C48.h5" ; sld:type cwl:File , xsd:string , sld:null . sld:type xsd:int , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default true ; sld:type xsd:boolean , sld:null . sld:default 500000 , 0 , 100000000000000000000 . sld:default 50 . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; sld:default "" ; sld:type xsd:string . sld:default "ion_ph" . sld:default "sol000/phase000" . sld:default "sol000/phase000" . a cwl:CommandLineTool ; rdfs:label "plot_demix_solutions" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "plot_demixing_solutions.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "plot_demix_solutions_err.log" ; cwl:stdout "plot_demix_solutions.log" . cwl:outputSource ; sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:int , sld:null . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . rdfs:label "mslin2circ" ; cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "ant" . sld:default true . sld:default "sol000/faraday" . rdfs:comment "Output Measurement Set" ; cwl:inputBinding [ CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . sld:default "Dysco" . rdfs:comment "will produce verbose output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "-v" ] ; sld:type xsd:boolean , sld:null . cwl:in , , , , , , , ; cwl:out , , ; cwl:run . sld:default true ; sld:type xsd:boolean , sld:null . sld:default 2 . rdfs:comment "Name of the output file" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--output_fname" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . sld:default "sol000/bandpass" . rdfs:comment "Output data column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:Directory . sld:default true . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Number of cpus, by default all available." ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "h5parm_cat" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(inputs.input_file.basename)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(inputs.input_file.basename)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(inputs.input_file.basename)" ] ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_file)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_file)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_file)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "h5parm_collector_output_err.log" ; cwl:stdout "h5parm_collector_output.log" . sld:default "time" , "freq" . a cwl:Workflow ; rdfs:label "faraday_rotation" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , . rdfs:label "losoto_plot_A1" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . sld:default 10 ; sld:type xsd:int , sld:null . sld:default "sol000/bandpass" . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default -3.14e+00 , 3.14e+00 . rdfs:comment "Uses an approximation stage in which the phases are constrained with the piece-wise fitter, to solve local minima problems." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approximatetec=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "resid" . sld:default "CORRECTED_DATA" . sld:default -3.14e+00 , 3.14e+00 . cwl:outputBinding [ CommandOutputBinding:glob "Ateam_separation.log" ] ; sld:type cwl:File . rdfs:comment "If mode = resid, this sets the reference antenna for phase solutions,\n by default None.\n" ; sld:type xsd:string , sld:null . cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "Keep duplicate components from model 1 or model 2" ; cwl:inputBinding [ CommandLineBinding:prefix "--keep=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "from2" ; sld:type xsd:string , sld:null . rdfs:comment "Skip setting the metadata correctly" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--skipmetadata" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Detect and remove bad channel before fitting, by default True." ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Instead of calculating rms of the rmses use this value\n(it will not be multiplied by the MaxRmsNoise), by default 0 (ignored).\n" ; sld:type xsd:float , sld:null . sld:default "time" , "freq" . sld:default 10 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.usebeammodel=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "List of files with flag information (JSON)" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "ion_ph-res" . sld:default "pol" . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . sld:default "CORRECTED_DATA" . rdfs:comment "overrides the number of threads specified in the strategy\n(default: one thread for each CPU core)\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-j" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default true . sld:default 20 ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "PolAlign" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:in , , ; cwl:out , ; cwl:run . sld:default "CORRECTED_DATA" . sld:default "" . rdfs:comment "Minimum number of visibilities within a solution interval" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.minvisratio=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . rdfs:comment "Maximum allowable width in number of samples (after regridding) above which\ninterpolated values are flagged (e.g., maxFlaggedWidth = 5 would allow gaps of\n5 samples or less to be interpolated across but gaps of 6 or more would be\nflagged)\n" ; sld:type xsd:int , sld:null . sld:default "calibrator" . rdfs:comment "define the maximum seperation between pointing and model direction in arcmin" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--max_separation_arcmin" ] ; sld:type xsd:float , sld:null . rdfs:comment "Detrending/fitting algorithm: smooth / poly / spline.\nBy default smooth.\n" ; sld:type xsd:string , sld:null . sld:default "ant" . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "HBA" ; sld:type xsd:string , sld:null . sld:default "calibrator" . sld:default "applybeam" . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$([self])" . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "time" , "freq" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*.png" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:Directory ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type cwl:File . sld:default false ; sld:type xsd:boolean , sld:null . sld:default 1e+00 ; sld:type xsd:float , sld:null . sld:default "CORRECTED_DATA" . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "CORRECTED_DATA" ; sld:type xsd:string , sld:null . rdfs:comment "Reference antenna for phases. By default None." ; sld:type xsd:string , sld:null . rdfs:comment "Name of the axis for which regridding/interpolation will be done" ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "BP" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File . sld:default "faraday" . cwl:outputBinding [ CommandOutputBinding:glob "DP3.parset" ] ; sld:type cwl:File . sld:default "time" , "freq" . sld:default true . rdfs:comment "Input measurement set" ; sld:type cwl:Directory . cwl:source ; cwl:valueFrom "$([self])" . cwl:inputBinding [ CommandLineBinding:prefix "--outmodel=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "output.skymodel" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:float , sld:null . cwl:source . cwl:source . sld:type cwl:Directory , cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default "pol" . rdfs:comment "Number of columns in a multi-table image. By default is automatically\nchosen.\n" ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "Change the the weight values.\nParameters\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('REWEIGHT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:source . rdfs:label "smoothb" ; cwl:in , , , , , ; cwl:out , ; cwl:run . rdfs:label "check_demix" ; cwl:in , , , , , , , ; cwl:out , , , , , , , ; cwl:run . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Fit a 3rd order ionospheric ocmponent (usefult <40 MHz). By default False.\n" ; sld:type xsd:boolean , sld:null . rdfs:comment "Input Measurement Set(s)" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.map(function(directory){ return directory.basename; }).join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.map(function(directory){ return directory.basename; }).join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.map(function(directory){ return directory.basename; }).join(','))]" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . rdfs:label "initial_flags_join" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:default "faraday" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--clip_sources" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self)" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "prep" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outmodel)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; sld:type cwl:File . sld:default "sol000/phaseOrig" . a cwl:Workflow ; rdfs:label "ion" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--demix_sources" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self)" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . sld:type cwl:File . sld:default "sol000/tec" . rdfs:label "concat_logfiles_calib" ; cwl:in , ; cwl:out ; cwl:run . sld:default "rotation+diagonal" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--structure_file" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . sld:default "polalign" . cwl:linkMerge "merge_flattened" ; cwl:outputSource , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . a cwl:CommandLineTool ; rdfs:comment "This operation for LoSoTo implement a flagging procedure\nWEIGHT: compliant\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('FLAG').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:label "concat_logfiles_beam" ; cwl:in , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . rdfs:comment "path extension of the sky models" ; sld:type xsd:string , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "3C48,3C147,3C196,3C295,3C380" ; sld:type xsd:string , sld:null . rdfs:comment "Median window size in number of timeslots for 'window' mode.\nIf nonzero, a median-smoothed version of the input values is\nsubtracted to detrend them. If 0, no smoothing or subtraction is\ndone, by default 3.\n" ; sld:type xsd:int , sld:null . sld:default "time" . cwl:pickValue "first_non_null" ; cwl:source , . cwl:source . sld:default "POINTING" ; sld:type xsd:string , sld:null . rdfs:comment "Propagate solutions of the previous time slot only if the solve converged" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagateconvergedonly=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . a cwl:Workflow ; rdfs:label "FR" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . sld:default "apply_cal_FR" . cwl:source . cwl:source . cwl:source . cwl:source . sld:default "sol000/phase000" . sld:type cwl:File . sld:default -3.14e+00 , 3.14e+00 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default "calib_cal_PA" . sld:default "polalign_rotangle" . cwl:source . sld:type cwl:File . rdfs:label "losoto_plot_B3" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . sld:default "ant" . rdfs:comment "Choose correlation to be reset" ; sld:type xsd:string , sld:null . sld:default "calibrator" . rdfs:label "concat_logfiles_RefAnt" ; cwl:in , ; cwl:out ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . cwl:in , , , , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:default "applybeam" . a cwl:CommandLineTool ; rdfs:comment "A smoothing function: running-median on an arbitrary number of axes, running\npolyfit and Savitzky-Golay on one axis, or set all solutions to the\nmean/median value.\nWEIGHT: flag ready.\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "run_losoto_smooth.sh" ) ; cwl:arguments ( "run_losoto_smooth.sh" ) ; cwl:arguments ( "run_losoto_smooth.sh" ) ; cwl:arguments ( "run_losoto_smooth.sh" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('SMOOTH').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_SMOOTH=$(inputs.execute)\nif [ \"$DO_SMOOTH\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped smoothing.\nfi\n" ; cwl:entryname "run_losoto_smooth.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_SMOOTH=$(inputs.execute)\nif [ \"$DO_SMOOTH\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped smoothing.\nfi\n" ; cwl:entryname "run_losoto_smooth.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('SMOOTH').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_SMOOTH=$(inputs.execute)\nif [ \"$DO_SMOOTH\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped smoothing.\nfi\n" ; cwl:entryname "run_losoto_smooth.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('SMOOTH').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('SMOOTH').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_SMOOTH=$(inputs.execute)\nif [ \"$DO_SMOOTH\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped smoothing.\nfi\n" ; cwl:entryname "run_losoto_smooth.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:source . sld:default "polalign" . sld:default "*&" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvmmax=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvmmax=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvmmax=" ; CommandLineBinding:separate false ] ; sld:default 1e+15 ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "output soltab name for tec" ; sld:type xsd:string , sld:null . rdfs:comment "verbose output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; sld:default true ; sld:type xsd:boolean . sld:default "phaseOrig" . cwl:source . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . sld:default true . cwl:source . rdfs:label "write_solutions" ; cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "summary" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "make_summary.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:stderr "summary_err.log" ; cwl:stdout "summary.log" . sld:default 0 ; sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . sld:default true . cwl:outputSource ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:comment "Duplicate a table\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('DUPLICATE').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . rdfs:label "h5parm_pointingname" ; cwl:in , , ; cwl:out , ; cwl:run . sld:default "phaseonly" . rdfs:comment "Window size for the runningmedian, savitzky-golay, and runningpoly (array\nof same size of axesToSmooth), by default [].\n" ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:source . sld:default "time" , "freq" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.beammode=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.beammode=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.beammode=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:default "clock" ; sld:type xsd:string , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:source . a cwl:ExpressionTool ; rdfs:label "selectfirstdirectory" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n return {'output': inputs.input[0]}\n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.input)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).demix_freqres)" ; cwl:loadContents true ] ; sld:type xsd:string . rdfs:comment "Tolerance at which the approximating first stage is considered to be converged and the second full-constraining stage is started." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approxtolerance=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approxtolerance=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approxtolerance=" ; CommandLineBinding:separate false ] ; sld:type xsd:float , sld:null . sld:default "195.3125kHz" ; sld:type xsd:string , sld:null . sld:default "bandpass" . sld:default "calibrator" . a cwl:CommandLineTool ; rdfs:label "plot_demix_noise_ratio" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "plot_demixing_noise.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:inputs , , ; cwl:outputs , . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . rdfs:comment "Number of cpu to use, by default all available." ; sld:type xsd:int , sld:null . cwl:source . sld:default "SMOOTHED_DATA" . cwl:source . sld:type cwl:File . sld:default "losoto" . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . sld:default 500000 , 0 , 100000000000000000000 . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; sld:type xsd:string , sld:null . rdfs:label "summary" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Will select either memory or direct mode based on available memory (default).\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-auto-read" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "mslin2circ*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "find_skymodel_cal.log" ] ; sld:type cwl:File . cwl:source . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "aoflag.log" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:default "YY" . sld:default true . sld:default true . cwl:source . cwl:source . rdfs:comment "List of h5parm files" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . sld:default "sol000/amplitude000" . cwl:source . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:comment "A list of lists specifying groups of antennas that are to be constrained to have the same solution." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.antennaconstraint=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.antennaconstraint=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.antennaconstraint=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Solution table" ; sld:type xsd:string . cwl:source . cwl:source . rdfs:label "concat_logfiles_blsmooth" ; cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Output h5parm" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; sld:type cwl:File . rdfs:label "applyFR" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . sld:default "findRefAnt" . rdfs:comment "MS set output" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . sld:default true . cwl:source . rdfs:comment "When unequal to 0, all stations within the given distance from the reference station (0) will be constrained to have the same solution (in metres)" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.coreconstraint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.coreconstraint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.coreconstraint=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . sld:default true . sld:type xsd:string , sld:null . rdfs:label "concat_logfiles_calib_cal" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . sld:default "Dysco" . rdfs:label "applyBP" ; cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . sld:default 20 ; sld:type xsd:int , sld:null . sld:default "merge_skymodels" . cwl:source . rdfs:comment "Standard deviation window size in number of timeslots for 'window' mode, by default 251." ; sld:type xsd:int , sld:null . cwl:source ; sld:default 20 . cwl:inputBinding [ cwl:valueFrom "$(self ? 1 : 0)" ] ; sld:type xsd:boolean , sld:null . sld:default true . sld:default "" ; sld:type xsd:string , sld:null . sld:default false . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "calib_cal" . rdfs:comment "Size of the window (diameter), per axis. If 0 is given then the entire\n length of the axis is assumed.\nMust be a vector of same length of Axes.\n" ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:type xsd:int , sld:null . rdfs:comment "saves used software versions in this LINC run\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--versions" ; CommandLineBinding:separate true ] ; sld:default "$LINC_DATA_ROOT/.versions" ; sld:type cwl:File , xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--outputimage" ] ; sld:default "Ateam_separation.png" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "TaQL" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "taql" ) ; cwl:baseCommand ( "taql" ) ; cwl:baseCommand ( "taql" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "taql_err.log" ; cwl:stdout "taql.log" . cwl:pickValue "all_non_null" ; cwl:source . rdfs:comment "Size of the markers in the 2D plot. By default 2.\n" ; sld:default 2 ; sld:type xsd:int , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Number of independent cycles of flag expansion, by default 3." ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Tabs to plot" ; sld:type xsd:string . cwl:source . cwl:source . sld:default "SET CIRC_PHASEDIFF_DATA[,0]=0.5*EXP(1.0i*(PHASE(CIRC_PHASEDIFF_DATA[,0])-PHASE(CIRC_PHASEDIFF_DATA[,3]))), CIRC_PHASEDIFF_DATA[,3]=CIRC_PHASEDIFF_DATA[,0], CIRC_PHASEDIFF_DATA[,1]=0+0i, CIRC_PHASEDIFF_DATA[,2]=0+0i" . rdfs:label "applyFR" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . sld:default 2000 ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "h5parm_pointingname" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "h5parm_pointingname.py" ) ; cwl:baseCommand ( "h5parm_pointingname.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parmFile)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parmFile)" ] ] ; cwl:stderr "h5parm_pointingname_err.log" ; cwl:stdout "h5parm_pointingname.log" . cwl:source . sld:default "ant" . sld:default "ant" . sld:default "ion.h5" . sld:default "*&" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[ddecal,count]" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:stderr "ddecal_err.log" ; cwl:stdout "ddecal.log" . sld:default "bandpass_transfer_" . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "Smooth only amplitudes" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-a" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-a" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-a" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-a" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "CORRECTED_DATA" . sld:type cwl:File . sld:default "CORRECTED_DATA" . sld:default "Dysco" . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "MS containing the calibrator" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:Directory ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Number of CPU used, by default all available." ; sld:type xsd:int , sld:null . sld:default true . sld:type xsd:boolean , sld:null . rdfs:label "H5parm_collector" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.type)*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.type)*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , ; cwl:out , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "check_demix.log" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:Directory . rdfs:comment "Output MS" ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Kernel size in Hz" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessconstraint=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . sld:default "sol000/phase000" . sld:default 10 ; sld:type xsd:int , sld:null . cwl:source . sld:default true . cwl:source . rdfs:label "aoflag" ; cwl:in , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Will read the entire measurement set in memory. This is the fastest,\nbut requires much memory.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-memory-read" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--Ateam_separation_file" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , , , , , , , , , . sld:default "pol" . rdfs:label "write_solutions" ; cwl:in , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . rdfs:comment "Min max value for the independent variable (0 means automatic).\n" ; sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . cwl:source . cwl:source . sld:default "freq" . cwl:source . cwl:source . sld:default "time" , "freq" . rdfs:label "losoto_plot_B1_trans" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "MODEL_DATA" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "log" ; sld:type xsd:string , sld:null . sld:default "median" . cwl:source . a cwl:Workflow ; rdfs:label "prepare_fr" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . sld:default "calibrator" . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . rdfs:label "transfer_solutions" ; cwl:in , , , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "List of h5parm files" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . rdfs:comment "Solution table" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "An optional reference frequency (in Hz) for the smoothness constraint" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessreffrequency=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . cwl:source . sld:default "calibrator" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.sourcedb=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File , sld:null . sld:default "ant" . rdfs:label "add_circ_phasedif" ; cwl:in , , , ; cwl:out , ; cwl:run . sld:type cwl:Directory . rdfs:comment "Mean-average in time the resulting delays/offset." ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; sld:type xsd:string , sld:null . sld:default "sol000/clock" . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Reference antenna, by default the first." ; sld:type xsd:string , sld:null . sld:default "ant" . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--instrument_tables" ; cwl:valueFrom "[$(self.map(function(directory){ return directory.path; }).join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "apply_pa_bandpass" . rdfs:label "apply_calibrate_bp" ; cwl:in , , , , , , ; cwl:out , , , , , , , ; cwl:run ; cwl:scatter ( ) . sld:default "sol000/phaseOrig" . cwl:outputBinding [ CommandOutputBinding:glob "h5parm_pointingname*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "h5parm_pointingname*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "*&" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Output Measurement Set" ; cwl:inputBinding [ CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . sld:default "cal_solutions.h5" . sld:default "calib_cal" . sld:default "amplitude000" . sld:default true . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--ionex" ; CommandLineBinding:separate true ; CommandLineBinding:shellQuote false ] ; sld:default "True" ; sld:type xsd:string , sld:null . rdfs:comment "Ignore baselines / channels with UV < uvlambdamin wavelengths." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvlambdamin=" ; CommandLineBinding:separate false ] ; sld:default 3e+02 ; sld:type xsd:float , sld:null . sld:default true . sld:default "ant" . sld:type cwl:File , sld:null . rdfs:comment "When unequal to 0, all stations within the given distance from the reference station (0) will be constrained to have the same solution (in metres)" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.coreconstraint=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . cwl:source . rdfs:comment "Do not smooth in frequency" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "BLsmooth" ; cwl:in , , ; cwl:out , ; cwl:run . sld:default "" . cwl:source . rdfs:comment "Note: this step uses the OrigClock solutions, to ensure that the\nunsmoothed clock is used to calculate the residuals\n" ; cwl:in , , ; cwl:out , ; cwl:run . sld:type xsd:string , sld:null . sld:default "DATA" . sld:default "bandpass_" . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name==\".\" ? inputs.msin.basename : inputs.msout_name)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parm.basename)" ] ; sld:type cwl:File . sld:default 8 . cwl:source . sld:default "element" . rdfs:comment "Specifies the telescope if mode = 'bandpass'." ; sld:type xsd:string , sld:null . sld:default -3.14e+00 , 3.14e+00 . sld:default "DATA" . sld:default 30 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Number of channels in each channel block, for which the solution is assumed to be constant." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.nchan=" ; CommandLineBinding:separate false ] ; sld:default 1 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usebeammodel=True" ; CommandLineBinding:separate false ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "msout.writefullresflag=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "sol000/phase000" . cwl:source . cwl:in , , , , , , , ; cwl:out , ; cwl:run . rdfs:label "losoto_plot_B2_trans" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , , , , , , , , , . sld:default 0 . cwl:source . rdfs:comment "Define output file name for JSON statistics" ; cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out.json" ; sld:type xsd:string , sld:null . sld:default "bandpass_transfer_" . cwl:source . cwl:source . rdfs:label "clocktec" ; cwl:in , , , , ; cwl:out , , ; cwl:run . rdfs:label "concat_logfiles_predict" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default true . rdfs:label "check_Ateam_separation" ; cwl:in , ; cwl:out , , ; cwl:run . sld:default "calibrator" . sld:default "time" . cwl:outputSource ; sld:type cwl:File . sld:default false . rdfs:comment "Output logfile" ; cwl:outputBinding [ CommandOutputBinding:glob "taql*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "taql*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "taql*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "summary*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "bandpass" ; cwl:in , , , , , , ; cwl:out , ; cwl:run . rdfs:label "concat_parset" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.invert=False" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.invert=False" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.invert=False" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.invert=False" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.invert=False" ; CommandLineBinding:separate false ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:default true . rdfs:comment "Propagate solutions of the previous time slot only if the solve converged" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagateconvergedonly=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagateconvergedonly=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagateconvergedonly=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default 0 . sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).demix == 0 ? false : true)" ; cwl:loadContents true ] ; sld:type xsd:boolean . sld:default "element" . cwl:source . sld:default "pol" . cwl:source . rdfs:comment "Comma separated list of (zero-indexed) band ids to process" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "-bands" ; CommandLineBinding:shellQuote false ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default "blsmooth_FR" . sld:default "tec3rd" . cwl:source . sld:default 0 . a cwl:Workflow ; rdfs:label "losoto_bandpass" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "plot_demix_solutions*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 0 . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . sld:default 10 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "output soltab name for phase offset" ; sld:type xsd:string , sld:null . sld:default "fr_ph_" . sld:default "bandpass_" . a cwl:CommandLineTool ; rdfs:label "check_demix" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "check_demix.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import json\nimport os\nimport lsmtool\nimport numpy, math\nnull = None\n\nfrom tune_demixing_parameters import main as tune_demixing_parameters\n\ntargets = {'CasA' : {'ra' : 6.123487680622104, 'dec' : 1.0265153995604648}, \\\n 'CygA' : {'ra' : 5.233686575770755, 'dec' : 0.7109409582180791}, \\\n 'TauA' : {'ra' : 1.4596748493730913, 'dec' : 0.38422502335921294}, \\\n 'HerA' : {'ra' : 4.4119087330382163, 'dec' : 0.087135562905816893}, \\\n 'VirA' : {'ra' : 3.276086511413598, 'dec' : 0.21626589533567378}, \\\n 'Sun' : {'ra' : 0, 'dec' : 0 }, \\\n 'Jupiter': {'ra' : 0, 'dec' : 0 }, \\\n 'Moon' : {'ra' : 0, 'dec' : 0 }}\n\n## set default values\nparameters = {'demixtimeresolution': 10, \\\n 'demixfreqresolution': 48820, \\\n 'maxiter': 20, \\\n 'lbfgs.historysize': 10, \\\n 'lbfgs.robustdof': 200}\n\ninputs = json.loads(r'''$(inputs)''')\n\ndemix = inputs['demix']\ndemix_sources = inputs['demix_sources']\nclip_sources = inputs['clip_sources']\nskymodel = inputs['skymodel']\ntarget_skymodel = inputs['target_skymodel'][\"path\"]\nfuzzy_config = inputs['fuzzy_config']\nAteam_separation_file = inputs['Ateam_separation_file'][\"path\"]\ntolerance_arcmin = 6.0\nclipAteam = inputs['clipAteam']\nmin_probability = inputs['min_probability']\n\nif not clipAteam:\n clip_sources = []\nif fuzzy_config is None:\n fuzzy_config = os.path.expandvars(\"$LINC_DATA_ROOT/configs/demix_fuzzy_config.json\")\nelse:\n fuzzy_config = fuzzy_config[\"path\"]\nif skymodel is None:\n skymodel = os.path.expandvars(\"$LINC_DATA_ROOT/skymodels/A-Team.skymodel\")\nelse:\n skymodel = skymodel[\"path\"]\ns = lsmtool.load(skymodel)\n\nf = open(Ateam_separation_file, 'r')\nAteam_separation = json.load(f)\nf.close()\n\ndemix_sources_fixed = True if demix == 1 else False ## stick to given selection, since user enforced it\n\nif demix is None: ## choose demix candidates according to the information given in the Ateam_separation_file\n demix = 0\n demix_list = []\n for item in Ateam_separation:\n ra = math.degrees(targets[item['source']]['ra'])\n dec = math.degrees(targets[item['source']]['dec'])\n dist_deg = s.getDistance(ra, dec, byPatch=True)\n if any(dist_deg * 60.0 < tolerance_arcmin):\n for index in numpy.where(dist_deg * 60 < tolerance_arcmin)[0]:\n patch_name = s.getPatchNames()[index]\n if patch_name in demix_sources:\n demix_list.append(patch_name)\n demix = 1\n demix_sources = demix_list\nelif demix == 0:\n demix_sources = []\nif demix == 1: ## determine demix parameters and remove sources to be demix if needed and allowed as well as determine sources to be clipped\n print(\"INFO: Will determine demixing parameters for: \" + str(demix_sources))\n parameters, info = tune_demixing_parameters(MS='*.MS', sky_model=skymodel, target_sky_model=target_skymodel, fuzzy_config=fuzzy_config, patch_list=demix_sources)\n if not demix_sources_fixed and len(demix_sources) > 1:\n for patch in [index for index,element in enumerate(info['probabilities']) if element < min_probability]:\n demix_sources.remove(info['patches'][patch])\n patches = s.getPatchPositions()\n clip_list = clip_sources.copy()\n for item in clip_list:\n (ra, dec) = patches[item]\n dist_deg = s.getDistance(ra.value, dec.value, byPatch=True)\n if any(dist_deg * 60.0 < 6.0):\n for index in numpy.where(dist_deg * 60 < tolerance_arcmin)[0]:\n patch_name = s.getPatchNames()[index]\n if patch_name in demix_sources:\n clip_sources.remove(item)\n\n## set demix to false again in case all sources have been deselected\nif len(demix_sources) == 0:\n demix = 0\n\nprint(\"Demixing will use the following parameters if not specified otherwise by the user:\", parameters)\nprint(\"The following sources will be demixed: \", demix_sources)\nprint(\"The following sources will be clipped: \", clip_sources)\n\n\ncwl_output = {'demix_sources' : demix_sources,\n 'clip_sources' : clip_sources,\n 'demix' : demix,\n 'demix_timeres' : parameters['demixtimeresolution'],\n 'demix_freqres' : str(parameters['demixfreqresolution'] * 10**(-3))+\"kHz\",\n 'demix_maxiter' : parameters['maxiter'],\n 'lbfgs_historysize': parameters['lbfgs.historysize'],\n 'lbfgs_robustdof' : parameters['lbfgs.robustdof']}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "check_demix.py" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "check_demix_err.log" ; cwl:stdout "check_demix.log" . cwl:source . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:in , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Output MS" ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default true . sld:default 4 ; sld:type xsd:int , sld:null . sld:default "ant" . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . cwl:source ; sld:default "CS001HBA0" . rdfs:comment "Invert (reverse the sign of) the phase offsets. By default False. Set to True\nif you want to use them with the residuals operation.\n" ; sld:type xsd:boolean , sld:null . sld:default "" ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$([self])" . cwl:source . rdfs:comment "Provide state information for collecting antenna statistics" ; sld:default "NONE" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Number of cores" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-n" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-n" ] ; sld:default 4 ; sld:type xsd:int , sld:null . sld:default "CIRC_PHASEDIFF_DATA" . cwl:in , , ; cwl:out , ; cwl:run . sld:default "sol000/amplitude000" . sld:type cwl:File . sld:type xsd:boolean , sld:null . rdfs:label "losoto_plot_Rot3" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . sld:default 2000 ; sld:type xsd:int , sld:null . rdfs:label "predict_calibrate" ; cwl:in , , , , , ; cwl:out , , , , , ; cwl:run ; cwl:scatter ( ) . rdfs:label "losoto_plot_B3_trans" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "max separation in arc minutes" ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "mslin2circ" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "mslin2circ.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "mslin2circ_err.log" ; cwl:stdout "mslin2circ.log" . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--MS" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default "amplitudeOrig001" . sld:default "fr_ph_res" . sld:default "sol000/amplitude000" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvmmax=" ; CommandLineBinding:separate false ] ; sld:default 1e+15 ; sld:type xsd:float , sld:null . sld:default "polalign_ph-res_" . cwl:source . rdfs:comment "Concatenate all input SBs on-the-fly" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-concatenate-frequency" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "OrigClock" . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Estimate polarization misalignment as delay\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('POLALIGN').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:default 200 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:label "get_fr_model" ; cwl:in , ; cwl:out , ; cwl:run . cwl:source . sld:default "3C48,3C147,3C196,3C295" ; sld:type xsd:string . sld:type cwl:File . rdfs:comment "Define output file name for JSON statistics" ; cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out.json" ; sld:type xsd:string , sld:null . sld:default "final" . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . sld:default "fr" . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[]" "msout=." ) ; cwl:arguments ( "steps=[]" "msout=." ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "dp3_addcol_err.log" ; cwl:stdout "dp3_addcol.log" . rdfs:comment "Reads uvw values (some exotic strategies require these)" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-uvw" ; CommandLineBinding:shellQuote false ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . sld:default "bandpass_transfer_" . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default false . sld:default 30 ; sld:type xsd:int , sld:null . rdfs:label "losoto_plot_B1" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . sld:default 30 ; sld:type xsd:int , sld:null . rdfs:comment "Specify column to flag" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-column" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:string , sld:null . sld:default "CIRC_PHASEDIFF_DATA" . sld:default "bandpass_" . sld:default true . cwl:source . sld:default 5e+06 . cwl:source . cwl:source . rdfs:label "concat_logfiles_plot_demix" ; cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.demix)" . rdfs:comment "Name of the input h5parm solution set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Output h5parm name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; sld:default "output.h5" ; sld:type xsd:string . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "demix_solutions_*.png" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:Directory . sld:default "dp3_prep_cal" . sld:default 1e+00 . rdfs:comment "overwrite output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:default false ; sld:type xsd:boolean . cwl:source . cwl:source . sld:default "time" , "freq" . sld:default "ant" . rdfs:label "applybeam" ; cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type cwl:Directory . cwl:source . rdfs:comment "Assume circular polarization with FR not removed. By default False.\n" ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "Axes used to compute the smoothing function." ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "find_skymodel_cal.py" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "find_sky.py" ) ; cwl:baseCommand ( "python3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport os\nimport shutil\nimport json\n\nfrom unittest.mock import MagicMock\nsys.modules['lofarpipe.support.data_map'] = MagicMock()\n\n\nfrom find_skymodel_cal import main as find_skymodel\n\nmss = sys.argv[1:]\ninputs = json.loads(r'''$(inputs)''')\n\nskymodels = inputs['skymodels']\nmax_separation_arcmin = inputs['max_separation_arcmin']\nmax_separation_arcmin = 1.0 if max_separation_arcmin is None else max_separation_arcmin\nextension = inputs['skymodels_extension']\nif skymodels is None:\n skymodels = os.path.expandvars(\"$LINC_DATA_ROOT/skymodels\")\nelse:\n skymodels = skymodels[\"path\"]\noutput = {}\nif extension is not None:\n output = find_skymodel(mss, skymodels, extension, max_separation_arcmin=max_separation_arcmin)\nelse:\n output = find_skymodel(mss, skymodels, max_separation_arcmin=max_separation_arcmin)\n\nskymodel_path = output['SkymodelCal']\nskymodel_name = output['SkymodelName']\nskymodel_path = shutil.copy(skymodel_path, os.getcwd())\ncwl_output = {'file':{'class': 'File', 'path': skymodel_path},\n 'skymodel_name': skymodel_name}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "find_sky.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "find_skymodel_cal_err.log" ; cwl:stdout "find_skymodel_cal.log" . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "merge_skymodels" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "merge_skymodels.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:stderr "merge_skymodels_err.log" ; cwl:stdout "merge_skymodels.log" . rdfs:comment "Solution table that will be reset" ; sld:type xsd:string . sld:default "bandpass" . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . rdfs:comment "Minimum number of visibilities within a solution interval" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.minvisratio=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.minvisratio=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.minvisratio=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . rdfs:comment "Order of the function fitted during detrending.\nArray must have same size of axesToFlag.\nIf mode=smooth these are the window of the running median (0=all axis).\n" ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Dictionary that contains the flagged fraction per station" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:source . rdfs:comment "Stepsize between iterations" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.stepsize=" ; CommandLineBinding:separate false ] ; sld:default 2e-01 ; sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "dp3_prep_cal" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . sld:default "*&" ; sld:type xsd:string , sld:null . rdfs:comment "Number of cpu to use, by default all available." ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "losoto_ion" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . rdfs:comment "Percent of flagged data around the point to flag it, by default 50." ; sld:type xsd:float , sld:null . sld:type cwl:Directory , cwl:File , sld:null . sld:default "applybeam_bandpass" . cwl:source . rdfs:label "concat_logfiles_bp" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Split the I/O in n chunks. If you run out of memory, set this to a value > 2." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:default 8 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Selection of antenna subarrays using reqular expression\n" ; sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "parset" . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "--inmodel1=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "$LINC_DATA_ROOT/skymodels/A-Team.skymodel" ; sld:type cwl:File , xsd:string , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:shellQuote false ] ; sld:type cwl:Directory . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:default 0 ; sld:type xsd:int , sld:null . sld:type cwl:File , xsd:string , sld:null . sld:default "polalign" . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . rdfs:comment "Unwrap phases." ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default true . sld:default "sol000/phase000" . cwl:source . cwl:source . rdfs:label "concat_logfiles_applycal" ; cwl:in , ; cwl:out ; cwl:run . rdfs:label "concat_logfiles_blsmooth" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).demix_sources)" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . rdfs:label "losoto_plot_tec3rd" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . cwl:source . rdfs:comment "Use Log=’XYZ’ to set which axes to put in Log.\n" ; sld:type xsd:string , sld:null . sld:default "DATA" . sld:default true . a cwl:CommandLineTool ; rdfs:comment "This operation resets all values of the selected solution tables.\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('RESET').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:default "sol000/amplitudeOrig000" . cwl:source . sld:default "ant" . rdfs:comment "Filter these antenna string from the processing." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--filtered_antennas" ] ; sld:default "*&" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).demix_timeres)" ; cwl:loadContents true ] ; sld:type xsd:float . cwl:source . rdfs:label "concat_logfiles_calib" ; cwl:in , ; cwl:out ; cwl:run . sld:default 1e-30 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . rdfs:label "concat_logfiles_skymodels" ; cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Reference antenna used" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--refant" ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:source . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . rdfs:comment "Output JSON" ; cwl:outputBinding [ CommandOutputBinding:glob "*.json" ] ; sld:type cwl:File . rdfs:label "losoto_plot_Pd" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "Use model data from the measurement set." ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.modeldatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Size of the image [x,y], if one of the values is 0, then it is\nautomatically chosen. By default automatic set.\n" ; sld:default 0 ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction)*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction)*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction)*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction)*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction)*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type xsd:string . sld:default "polalign" . cwl:source . rdfs:comment "Summary File in JSON format" ; cwl:outputBinding [ CommandOutputBinding:glob "*.json" ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:Directory . cwl:source . sld:default "sol000/tec3rd" . sld:default "sol000/amplitude000" . rdfs:comment "Name of the input h5parm solution set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; sld:type xsd:string , sld:null . rdfs:comment "Make aoflagger reorder the measurement set before running the detection.\nThis prevents that aoflagger will use its memory reading mode, which is faster but uses more memory.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-reorder" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . rdfs:label "h5parm_pointingname" ; cwl:in , , ; cwl:out , ; cwl:run . sld:type cwl:File . cwl:source . rdfs:comment "Input Measurement Set string (including dummy.ms)" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . rdfs:comment "Reverse the time axis. By default False." ; sld:type xsd:boolean , sld:null . sld:default "polalign_ph_" . rdfs:comment "Make a movie summing up all the produced plots.\n" ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:default "tec" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:int , sld:null . sld:default "CasA_Gaussian" , "CygA_Gaussian" , "TauA_Gaussian" , "VirA_Gaussian" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "output table name (same solset)" ; sld:default "phasediff" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "linc_calibrator" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . rdfs:label "make_parset" ; cwl:in , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "Baselines to be selected" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . sld:default 1e-03 . rdfs:label "losoto_plot_clock" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . cwl:source . sld:default true . rdfs:label "select_only_first" ; cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . rdfs:comment "Output h5parm name" ; sld:default "output.h5" ; sld:type cwl:File . sld:type cwl:Directory , cwl:File . sld:default false . cwl:source . sld:default "model_fr" . rdfs:comment "Gives an indication on how the smoothing varies with" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-s" ] ; sld:default 1e+00 ; sld:type xsd:float , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . sld:default "True" . cwl:source . sld:default 1.2e+08 ; sld:type xsd:float . rdfs:label "applyPA" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "predict_cal*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:label "concat_logfiles_blsmooth" ; cwl:in , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self+'_summary')" . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "[FUSPID].*" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.invert=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.invert=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "*&" ; sld:type xsd:string , sld:null . sld:default "polalign_ph-res_poldif" . sld:default "CORRECTED_DATA" . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . rdfs:label "concat_logfiles_model" ; cwl:in , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 5e-01 ; sld:type xsd:float , sld:null . rdfs:comment "This must be a len=2 axis and the plot will have the differential value\n- e.g. ‘pol’ to plot XX-YY.\n" ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "apply_pa" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , , , , . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Input Measurement Set string (including dummy.ms)" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default true . rdfs:label "losoto_plot_A2" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . sld:default "*&" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[ddecal,count]" ) ; cwl:arguments ( "steps=[ddecal,count]" ) ; cwl:arguments ( "steps=[ddecal,count]" ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "ddecal_err.log" ; cwl:stdout "ddecal.log" . cwl:source . sld:default "model_fr" . rdfs:comment "Output h5parm" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parmFile.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parmFile.basename)" ] ; sld:type cwl:File . rdfs:comment "Do a running rms and then flag those regions that have a rms higher\nthan MaxRmsNoise*rms_of_rmses, by default 0 (ignored).\n" ; sld:type xsd:float , sld:null . cwl:source . sld:default true . sld:default 200 , 80 . sld:default false . cwl:source . rdfs:comment "removes all axes with the length of 1" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; sld:default false ; sld:type xsd:boolean . rdfs:label "concat_logfiles_applyFR" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Input main task name" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "'" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "'" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "'" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "UPDATE" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , , , , ; cwl:pickValue "all_non_null" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usebeammodel=True" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usebeammodel=True" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usebeammodel=True" ; CommandLineBinding:separate false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , , , , ; cwl:out , ; cwl:run . sld:default "*&" ; sld:type xsd:string , sld:null . rdfs:label "findRefAnt_join" ; cwl:in , ; cwl:out , ; cwl:run . cwl:source . sld:type cwl:File . cwl:source . sld:default "HBA" ; sld:type xsd:string , sld:null . sld:default "sol000/amplitude000" . sld:default "clock" . rdfs:comment "Matching radius in degrees for identifying duplicate components" ; cwl:inputBinding [ CommandLineBinding:prefix "--radius=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default 8.33e-03 ; sld:type xsd:float , sld:null . rdfs:label "concat_logfiles_applyBP" ; cwl:in , ; cwl:out ; cwl:run . sld:default "FR_MODEL_DATA" . sld:default 1 . sld:default "median" . cwl:source . rdfs:comment "Join all SPWs together in frequency direction before flagging" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-combine-spws" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$(self == \"LBA\" ? 54e6 : 12e7)" . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:source . sld:default "CORRECTED_DATA" . a cwl:Workflow ; rdfs:label "apply_calibrate" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , , , , , , . cwl:outputBinding [ CommandOutputBinding:glob "BLsmooth.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "BLsmooth.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "BLsmooth.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "BLsmooth.log" ] ; sld:type cwl:File . cwl:source . sld:default "time" , "freq" . sld:default 200 ; sld:type xsd:float , sld:null . sld:default 0 . rdfs:label "concat_logfiles_apply_fr" ; cwl:in , ; cwl:out ; cwl:run . sld:default -1e+00 ; sld:type xsd:float , sld:null . cwl:source . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . rdfs:label "losoto_plot_A3" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "Save the newly computed WEIGHT_SPECTRUM, this action permanently modify the MS!" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-w" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-w" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-w" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-w" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "concat_logfiles_calib_cal" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:Directory . rdfs:label "BLsmooth" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "Use model data from the measurement set." ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.modeldatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.modeldatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.modeldatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "sol000/phase000" . cwl:outputSource ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . sld:default true . sld:default "sol000/amplitude000" . sld:default true . cwl:source . cwl:source . rdfs:comment "Name of the output h5parm solution set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsoltab" ] ; sld:type xsd:string , sld:null . sld:default 30 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Initialize solver with the solutions of the previous time slot" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagatesolutions=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default true . cwl:source . sld:default "MODEL_DATA" . cwl:source . sld:type cwl:File . sld:default "time" , "freq" . cwl:pickValue "first_non_null" ; cwl:source , . sld:default 1 . rdfs:label "find_skymodel_cal" ; cwl:in , , ; cwl:out , , ; cwl:run . sld:default true . sld:default 1e-30 ; sld:type xsd:float , sld:null . sld:default "time" , "freq" . rdfs:comment "Flag only the unconverged solutions for which divergence was detected.\nAt the moment, this option is effective only for rotation+diagonal\nsolves, where divergence is detected when the amplitudes of any station\nare found to be more than a factor of 5 from the mean amplitude over all\nstations.\nIf divergence for any one station is detected, all stations are flagged\nfor that solution interval. Only effective when flagunconverged=true\nand mode=rotation+diagonal.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagdivergedonly=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . cwl:source . sld:default "sol000/phaseOrig" . cwl:outputSource ; sld:type xsd:string , sld:null . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . sld:default 100 , 40 . sld:type cwl:File . rdfs:comment "Tolerance at which the approximating first stage is considered to be converged and the second full-constraining stage is started." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approxtolerance=" ; CommandLineBinding:separate false ] ; sld:type xsd:float , sld:null . rdfs:comment "Maximum acceptable rms of the residuals in radians before flagging. Set to zero to avoid the check." ; sld:default 1 ; sld:type xsd:float , sld:null . sld:default "sol000/amplitude000" . sld:default false ; sld:type xsd:boolean , sld:null . sld:type xsd:float , sld:null . sld:default "" . rdfs:comment "Choose correlation to be plotted (XX,YY,XY,YX)\n" ; sld:type xsd:string , sld:null . rdfs:label "apply_pa" ; cwl:in , , , , ; cwl:out , , , , ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type cwl:File . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:label "add_fr_model" ; cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.sourcedb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.sourcedb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.sourcedb=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File , sld:null . rdfs:comment "List of directions to calibrate on" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.directions=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.directions=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.directions=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Number of channels in each channel block, for which the solution is assumed to be constant." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.nchan=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.nchan=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.nchan=" ; CommandLineBinding:separate false ] ; sld:default 1 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; sld:type cwl:File . sld:default "POINTING" ; sld:type xsd:string , sld:null . rdfs:comment "Prefix to add before the self-generated filename.\n" ; sld:default "losoto.plot." ; sld:type xsd:string , sld:null . sld:default "time" , "freq" . rdfs:comment "H5parm to which the solutions should be transferred." ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:default "output.h5" ; sld:type cwl:File . rdfs:comment "Maximum number of iterations during approximating stage" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxapproxiter=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxapproxiter=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxapproxiter=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "findRefAnt_join" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "findRefAnt_join.py" ) ; cwl:baseCommand ( "python3" "findRefAnt_join.py" ) ; cwl:baseCommand ( "python3" "findRefAnt_join.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(inputs.flagged_fraction_dict)" ; cwl:entryname "input.json" ] ; cwl:listing [ cwl:entry "import sys\nimport json\nimport re\nimport ast\n\ninputs = json.loads(r'''$(inputs)''')\nwith open('input.json', 'r') as f_stream:\n flagged_fraction_dict_list = json.load(f_stream)\nfilter_station = inputs['filter_station']\nno_station_selected = True\n\nwhile no_station_selected:\n print('Applying station filter ' + str(filter_station))\n flagged_fraction_data = {}\n no_station_selected = False\n for flagged_fraction_dict in flagged_fraction_dict_list:\n entry = ast.literal_eval(flagged_fraction_dict)\n antennas = entry.keys()\n selected_stations = [ station_name for station_name in antennas if re.match(filter_station, station_name) ]\n if len(selected_stations) == 0:\n print('No stations left after filtering. Station(s) do(es) not exist in all subbands. No filter is used.')\n filter_station = ''\n no_station_selected = True\n break\n for antenna in selected_stations:\n try:\n flagged_fraction_data[antenna].append(float(entry[antenna]))\n except KeyError:\n flagged_fraction_data[antenna] = [float(entry[antenna])]\n\nflagged_fraction_list = []\nsorted_stations = sorted(flagged_fraction_data.keys())\n\nflagged_fraction_antenna = {}\n\nfor antenna in sorted_stations:\n flagged_fraction = sum(flagged_fraction_data[antenna]) / len(flagged_fraction_data[antenna])\n flagged_fraction_list.append(flagged_fraction)\n flagged_fraction_antenna[antenna] = flagged_fraction\n try:\n flagged_fraction_data[flagged_fraction].append(antenna)\n except KeyError:\n flagged_fraction_data[flagged_fraction] = [antenna]\n\nmin_flagged_fraction = min(flagged_fraction_list)\nrefant = flagged_fraction_data[min_flagged_fraction][0]\nprint('Selected station ' + str(refant) + ' as reference antenna. Fraction of flagged data is ' + '{:>3}'.format('{:.1f}'.format(100 * min_flagged_fraction) + '%'))\n\nflagged_fraction_antenna['state'] = inputs['state']\n\ncwl_output = {'refant': str(refant)}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n\nwith open('./flagged_fraction_antenna.json', 'w') as fp:\n json.dump(flagged_fraction_antenna, fp)\n" ; cwl:entryname "findRefAnt_join.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nimport re\nimport ast\n\ninputs = json.loads(r'''$(inputs)''')\nwith open('input.json', 'r') as f_stream:\n flagged_fraction_dict_list = json.load(f_stream)\nfilter_station = inputs['filter_station']\nno_station_selected = True\n\nwhile no_station_selected:\n print('Applying station filter ' + str(filter_station))\n flagged_fraction_data = {}\n no_station_selected = False\n for flagged_fraction_dict in flagged_fraction_dict_list:\n entry = ast.literal_eval(flagged_fraction_dict)\n antennas = entry.keys()\n selected_stations = [ station_name for station_name in antennas if re.match(filter_station, station_name) ]\n if len(selected_stations) == 0:\n print('No stations left after filtering. Station(s) do(es) not exist in all subbands. No filter is used.')\n filter_station = ''\n no_station_selected = True\n break\n for antenna in selected_stations:\n try:\n flagged_fraction_data[antenna].append(float(entry[antenna]))\n except KeyError:\n flagged_fraction_data[antenna] = [float(entry[antenna])]\n\nflagged_fraction_list = []\nsorted_stations = sorted(flagged_fraction_data.keys())\n\nflagged_fraction_antenna = {}\n\nfor antenna in sorted_stations:\n flagged_fraction = sum(flagged_fraction_data[antenna]) / len(flagged_fraction_data[antenna])\n flagged_fraction_list.append(flagged_fraction)\n flagged_fraction_antenna[antenna] = flagged_fraction\n try:\n flagged_fraction_data[flagged_fraction].append(antenna)\n except KeyError:\n flagged_fraction_data[flagged_fraction] = [antenna]\n\nmin_flagged_fraction = min(flagged_fraction_list)\nrefant = flagged_fraction_data[min_flagged_fraction][0]\nprint('Selected station ' + str(refant) + ' as reference antenna. Fraction of flagged data is ' + '{:>3}'.format('{:.1f}'.format(100 * min_flagged_fraction) + '%'))\n\nflagged_fraction_antenna['state'] = inputs['state']\n\ncwl_output = {'refant': str(refant)}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n\nwith open('./flagged_fraction_antenna.json', 'w') as fp:\n json.dump(flagged_fraction_antenna, fp)\n" ; cwl:entryname "findRefAnt_join.py" ] ; cwl:listing [ cwl:entry "$(inputs.flagged_fraction_dict)" ; cwl:entryname "input.json" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nimport re\nimport ast\n\ninputs = json.loads(r'''$(inputs)''')\nwith open('input.json', 'r') as f_stream:\n flagged_fraction_dict_list = json.load(f_stream)\nfilter_station = inputs['filter_station']\nno_station_selected = True\n\nwhile no_station_selected:\n print('Applying station filter ' + str(filter_station))\n flagged_fraction_data = {}\n no_station_selected = False\n for flagged_fraction_dict in flagged_fraction_dict_list:\n entry = ast.literal_eval(flagged_fraction_dict)\n antennas = entry.keys()\n selected_stations = [ station_name for station_name in antennas if re.match(filter_station, station_name) ]\n if len(selected_stations) == 0:\n print('No stations left after filtering. Station(s) do(es) not exist in all subbands. No filter is used.')\n filter_station = ''\n no_station_selected = True\n break\n for antenna in selected_stations:\n try:\n flagged_fraction_data[antenna].append(float(entry[antenna]))\n except KeyError:\n flagged_fraction_data[antenna] = [float(entry[antenna])]\n\nflagged_fraction_list = []\nsorted_stations = sorted(flagged_fraction_data.keys())\n\nflagged_fraction_antenna = {}\n\nfor antenna in sorted_stations:\n flagged_fraction = sum(flagged_fraction_data[antenna]) / len(flagged_fraction_data[antenna])\n flagged_fraction_list.append(flagged_fraction)\n flagged_fraction_antenna[antenna] = flagged_fraction\n try:\n flagged_fraction_data[flagged_fraction].append(antenna)\n except KeyError:\n flagged_fraction_data[flagged_fraction] = [antenna]\n\nmin_flagged_fraction = min(flagged_fraction_list)\nrefant = flagged_fraction_data[min_flagged_fraction][0]\nprint('Selected station ' + str(refant) + ' as reference antenna. Fraction of flagged data is ' + '{:>3}'.format('{:.1f}'.format(100 * min_flagged_fraction) + '%'))\n\nflagged_fraction_antenna['state'] = inputs['state']\n\ncwl_output = {'refant': str(refant)}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n\nwith open('./flagged_fraction_antenna.json', 'w') as fp:\n json.dump(flagged_fraction_antenna, fp)\n" ; cwl:entryname "findRefAnt_join.py" ] ; cwl:listing [ cwl:entry "$(inputs.flagged_fraction_dict)" ; cwl:entryname "input.json" ] ] ; cwl:stderr "findRefAnt_err.log" ; cwl:stdout "findRefAnt.log" . sld:default true . sld:default "sol000/phase000" . sld:type cwl:File . rdfs:comment "Name of a soltab. Copy weights from this soltab (must have same axes shape), by default none." ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default 1 . sld:default "polalign.h5" . rdfs:label "losoto_plot_fr" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . sld:type xsd:string , sld:null . sld:default "Dysco" . cwl:in , , ; cwl:out , ; cwl:run . sld:default "sol000/OrigClock" . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default "Dysco" . rdfs:comment "Do not backup the old WEIGHT_SPECTRUM in WEIGHT_SPECTRUM_ORIG" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-b" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-b" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-b" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-b" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Minimum allowable fraction of new flagged frequencies. Stations with\nlower fractions will not have any new flags applied\n" ; sld:type xsd:float , sld:null . sld:default 10 ; sld:type xsd:float , sld:null . sld:default "ant" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "maximum amount of threads to be used for processing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[applycal, count]" "msout=." ) ; cwl:arguments ( "steps=[applycal, count]" "msout=." ) ; cwl:arguments ( "steps=[applycal, count]" "msout=." ) ; cwl:arguments ( "steps=[applycal, count]" "msout=." ) ; cwl:arguments ( "steps=[applycal, count]" "msout=." ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "applycal_$(inputs.correction)_err.log" ; cwl:stdout "applycal_$(inputs.correction).log" . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--outfile" ] ; sld:default "demix_noise_ratio.png" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:int , sld:null . rdfs:label "write_solutions" ; cwl:in , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solsetName" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solsetName" ] ; sld:default "target" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Flag unconverged solutions (i.e., those from solves that did not converge\nwithin maxiter iterations).\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagunconverged=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagunconverged=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagunconverged=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.sources=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self)]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Axes along which to smooth+find outlier (e.g. ['time', 'freq']), max 2 values." ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Assume that together with a delay each station has also a differential phase offset (important for old LBA observations)." ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default -3.14e+00 , 3.14e+00 . sld:default "calib_cal_FR" . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . rdfs:comment "Reference antenna for phases. By default None.\n" ; sld:default "" ; sld:type xsd:string , sld:null . rdfs:comment "This will split the set into intervals with the given maximum size, and flag each interval independently" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-chunk-size" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:int , sld:null . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Name of the output h5parm solution set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; sld:type xsd:string , sld:null . sld:default "195.3125kHz" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory . sld:default "losoto_FR" . rdfs:label "remove_col" ; cwl:in , , ; cwl:out , ; cwl:run . sld:default "Dysco" . cwl:source . sld:default 3e-01 . sld:default "apply_cal_bandpass" . cwl:source . rdfs:comment "Solution table" ; sld:type xsd:string . rdfs:label "merge_skymodels" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "minimum fraction of unflagged data per band to continue" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--min_unflagged" ] ; sld:default 5e-01 ; sld:type xsd:float , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "msout.overwrite=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Ignore baselines / channels with UV < uvlambdamin wavelengths." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvlambdamin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvlambdamin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.uvlambdamin=" ; CommandLineBinding:separate false ] ; sld:default 3e+02 ; sld:type xsd:float , sld:null . rdfs:comment "clip is done in log10 space, by default False" ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "time" , "freq" . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default "polalign_ph_poldif" . cwl:source . sld:default true . rdfs:comment "Output data column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . cwl:source . cwl:source . rdfs:label "concat_logfiles_model" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*.png" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "time" , "freq" . rdfs:comment "Kernel size in Hz" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessconstraint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessconstraint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessconstraint=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . sld:default 20 ; sld:type xsd:int , sld:null . rdfs:comment "A list of lists specifying groups of antennas that are to be constrained to have the same solution." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.antennaconstraint=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "List of h5parm files" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . rdfs:comment "Flag only the unconverged solutions for which divergence was detected.\nAt the moment, this option is effective only for rotation+diagonal\nsolves, where divergence is detected when the amplitudes of any station\nare found to be more than a factor of 5 from the mean amplitude over all\nstations.\nIf divergence for any one station is detected, all stations are flagged\nfor that solution interval. Only effective when flagunconverged=true\nand mode=rotation+diagonal.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagdivergedonly=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagdivergedonly=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagdivergedonly=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.overwrite=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , , ; cwl:out , , ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . sld:type xsd:string , sld:null . rdfs:comment "Flag zeros/ones (bad solutions in BBS/DP3). They should be flagged at import time. By default False." ; sld:type xsd:boolean , sld:null . sld:type cwl:File . rdfs:comment "Filter these baselines for the comparison" ; sld:default "*&" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).clip_sources)" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:label "FR" ; cwl:in , , , , , , , , , ; cwl:out , , , , , , ; cwl:run . cwl:source . sld:default "calib_cal_prep" . rdfs:comment "Initialize solver with the solutions of the previous time slot" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagatesolutions=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagatesolutions=True" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.propagatesolutions=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--removed_bands" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self)" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . rdfs:comment "Comma separated list of (zero-indexed) field ids to process" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "-fields" ; CommandLineBinding:shellQuote false ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "check_Ateam_separation" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "check_Ateam_separation.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InlineJavascriptRequirement ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , ; cwl:outputs , , ; cwl:stdout "Ateam_separation.log" . sld:default "MODEL_DATA" . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "Dysco" . rdfs:label "concat_logfiles_calib" ; cwl:in , ; cwl:out ; cwl:run . rdfs:label "BP" ; cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default "Dysco" . cwl:outputBinding [ CommandOutputBinding:glob "transfer_solutions*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.updateweights=True" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.updateweights=True" ; CommandLineBinding:separate false ] ; sld:type xsd:boolean , sld:null . rdfs:comment "What storage manager to use." ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . rdfs:comment "One of 'uniform' (single value), 'window' (sliding window in time), or 'copy' (copy from another table), by default 'uniform'." ; sld:default "uniform" ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . rdfs:comment "Return the ratio instead of subtracting." ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "msout.writefullresflag=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . rdfs:comment "Regular expression of antenna solutions to be transferred" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--antenna" ] ; sld:type xsd:string , sld:null . sld:default "sol000/amplitudeOrig001" . sld:default true . sld:default "savitzky-golay" . cwl:outputSource ; sld:type cwl:File . rdfs:comment "data value to be set" ; sld:default 0e+00 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ] ; sld:default "" ; sld:type xsd:string . cwl:source . rdfs:comment "If true performs smoothing" ; cwl:inputBinding [ CommandLineBinding:prefix "-S" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self ? 'True': 'False')" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-S" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self ? 'True': 'False')" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-S" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self ? 'True': 'False')" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-S" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self ? 'True': 'False')" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default "smooth" . sld:default 20 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "maximum amount of threads to be used for processing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . sld:default "DATA" . sld:default "bandpass" . rdfs:comment "2-element array of the median amplitude level to be acceptable,\n ampRange[0]: lower limit, ampRange[1]: upper limit.\nIf None or [0, 0], a reasonable range for typical observations is used.\n" ; sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . rdfs:label "concat_logfiles_predict" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default false . a cwl:Workflow ; rdfs:label "apply_calibrate" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , , , . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:default "dp3" . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , , , , . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Solution table" ; sld:type xsd:string . sld:default 500000 , 0 , 100000000000000000000 . sld:default true . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.beammode=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.beammode=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:label "concat_logfiles_summary" ; cwl:in , ; cwl:out ; cwl:run . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . cwl:source . cwl:pickValue "first_non_null" ; cwl:source , . cwl:source . sld:default 0e+00 . sld:default "blsmooth_PA" . rdfs:comment "Flag unconverged solutions (i.e., those from solves that did not converge\nwithin maxiter iterations).\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.flagunconverged=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Stepsize between iterations" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.stepsize=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.stepsize=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.stepsize=" ; CommandLineBinding:separate false ] ; sld:default 2e-01 ; sld:type xsd:float , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Fundamental width between samples after regridding. E.g., \"100kHz\" or \"10s\"" ; sld:default "100kHz" ; sld:type xsd:string , sld:null . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default true . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:label "flag" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "polalign" . rdfs:comment "The axis to plot in different colours - e.g. pol to get correlations with\n different colors.\n" ; sld:type xsd:string , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "DP3*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 1e-30 ; sld:type xsd:float , sld:null . rdfs:comment "Filename of output H5Parm (to be read by e.g. losoto)" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name_h5parm)" ] ; sld:type cwl:File . rdfs:comment "Parset for plotting diagnostic plots after transfer with LoSoTo" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--parset" ] ; sld:type cwl:File , sld:null . rdfs:comment "Axes used to find close flags." ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "the axis to plot on a page - e.g. ant to get all antenna’s on one file.\n" ; sld:type xsd:string , sld:null . sld:default "applycal" . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . rdfs:comment "Baselines to be selected" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:default "time" . cwl:source . rdfs:comment "Output Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "." ; sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:comment "Replace bad values with the interpolated ones,\ninstead of flagging them. By default False.\n" ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . rdfs:comment "verbose output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; sld:default true ; sld:type xsd:boolean . cwl:source ; sld:default 10 . sld:default "ant" . cwl:source . sld:type cwl:File . rdfs:label "dp3_prep_cal" ; cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:default "applycal" . sld:default -1e+00 ; sld:type xsd:float , sld:null . sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.basename+\":CIRC_PHASEDIFF_DATA\")" . cwl:source . cwl:source ; sld:default false . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "List of soltabs to subtract" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default 10 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "flagged_fraction_antenna.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "flagged_fraction_antenna.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "flagged_fraction_antenna.json" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "AOFlagger" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "aoflagger" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "aoflag_err.log" ; cwl:stdout "aoflag.log" . cwl:source . cwl:outputSource , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; sld:default "12.21kHz" . cwl:outputSource ; sld:type cwl:File . sld:default true . cwl:source . cwl:source ; cwl:valueFrom "$(self == \"LBA\" ? 1e-2 : 0.2e-3)" . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "losoto_plot_Align" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . cwl:source . sld:default 30 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:default "sol000/bandpass" . cwl:outputBinding [ CommandOutputBinding:glob "h5parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "h5parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "h5parm_collector_output*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "calibrator" . cwl:source . sld:default true . sld:type xsd:float , sld:null . sld:default "calibrator" . cwl:source . rdfs:comment "What storage manager to use." ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "SMOOTHED_DATA" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[applybeam,count]" "msout=." ) ; cwl:arguments ( "steps=[applybeam,count]" "msout=." ) ; cwl:baseCommand ( "DP3" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:stderr "applycal_$(inputs.type)_err.log" ; cwl:stdout "applycal_$(inputs.type).log" . sld:default "sol000/phase000" . sld:default 4 ; sld:type xsd:int , sld:null . rdfs:label "applyPA" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Type of constraint to apply. Options are\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.mode=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.mode=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.mode=" ; CommandLineBinding:separate false ] ; sld:type [ sld:symbols , , , , , , , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , , , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , , , , , , , ; sld:type sld:enum ] . cwl:source . rdfs:comment "Output table name. By default choose next available from table type." ; sld:type xsd:string , sld:null . rdfs:comment "Save statistics as JSON file" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "concat_logfiles_PA" ; cwl:in , ; cwl:out ; cwl:run . sld:default "calibrator" . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . rdfs:comment "This sets the maximum allowable fraction of flagged solutions above\nwhich the entire station is flagged.\n" ; sld:type xsd:float , sld:null . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.msin)" ] ; sld:type cwl:Directory . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "predict" . rdfs:label "losoto_plot_Pr" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:shellQuote false ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Find a combined polarization solution, by default False.\n" ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "freq" . rdfs:comment "Convert from circular to linear" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reverse" ] ; sld:default false ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[predict,count]" "msout=." ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:stderr "predict_cal_err.log" ; cwl:stdout "predict_cal.log" . sld:type cwl:File . sld:default "freq" . rdfs:label "losoto_plot_P3" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . rdfs:label "FaradayRot" ; cwl:in , ; cwl:out , ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . rdfs:comment "Enable/disable the task" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--do_transfer True" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Antenna string to be processed" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--bad_antennas" ] ; sld:default "*&" ; sld:type xsd:string , sld:null . sld:default true . sld:default "calib_cal" . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Filename of output H5Parm (to be read by e.g. losoto)" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name_h5parm)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name_h5parm)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name_h5parm)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . rdfs:label "concat_logfiles_apply" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default "time" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Optional extra data columns to read" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.extradatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.extradatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.extradatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "maximum amount of threads to be used for processing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . rdfs:comment "Type of constraint to apply. Options are\n" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.mode=" ; CommandLineBinding:separate false ] ; sld:type [ sld:symbols , , , , , , , , , , , ; sld:type sld:enum ] . cwl:source . rdfs:label "plot_demix_noise_ratio" ; cwl:in , ; cwl:out , ; cwl:run ; cwl:when "$(inputs.demix)" . rdfs:comment "Tables to “add” (e.g. ‘sol000/tec000’), it works only for tec and clock\n to be added to phases.\n" ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:default "time" . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:source . sld:default "CIRC_PHASEDIFF_DATA" . sld:default "time" , "freq" . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "concat_logfiles_applyPA" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Solution table" ; sld:type xsd:string . sld:default "bandpass" . sld:default "losoto_ion" . sld:default "phase_offset" . sld:default "LINC" . sld:default "array_factor" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . sld:default "XX" . sld:default "ant" . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "SET FR_MODEL_DATA[,0]=0.5+0i, FR_MODEL_DATA[,1]=0.0+0i, FR_MODEL_DATA[,2]=0.0+0i, FR_MODEL_DATA[,3]=0.5+0i" . cwl:pickValue "first_non_null" ; cwl:source , . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "applybeam_PA" . sld:type cwl:File . cwl:source . sld:default true . sld:default "ant" . a cwl:Workflow ; rdfs:label "PA" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . sld:default "tec3rd" . rdfs:comment "Weights are updated to reflect the combined polarization (cannot be undone with -r)" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--weights" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:float , sld:null . cwl:source . rdfs:comment "Output column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ] ; sld:default "SMOOTHED_DATA" ; sld:type xsd:string , sld:null . cwl:source . sld:default true . rdfs:comment "List of directions to calibrate on" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.directions=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default 0 . cwl:pickValue "first_non_null" ; cwl:source , . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "MS set output" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:comment "Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase." ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('RESIDUALS').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('RESIDUALS').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('RESIDUALS').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:source . rdfs:label "concat_logfiles_apply_pa" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . sld:default -1 ; sld:type xsd:float , sld:null . rdfs:label "H5parm_collector" ; cwl:in , , , , ; cwl:out , ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "sol000/phase000" . sld:default "*&" ; sld:type xsd:string , sld:null . sld:default "freq" . sld:default "amplitudeOrig000" . cwl:source . sld:default 0 . rdfs:comment "Interpolation is done in log10 space, by default False" ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "time" . rdfs:label "losoto_plot_tec" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "Name of the pointing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--pointing" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--pointing" ] ; sld:default "POINTING" ; sld:type xsd:string , sld:null . rdfs:comment "Solution table" ; sld:type xsd:string . cwl:source . cwl:source . sld:default 100 . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "This operation for LoSoTo implements basic plotting WEIGHT:\n flag-only compliant, no need for weight\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:arguments ( "run_losoto_plot.sh" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:baseCommand ( "bash" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:source . cwl:source . cwl:source . rdfs:comment "output soltab name for clock" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , , , , , , , , . rdfs:comment "Output logfile" ; cwl:outputBinding [ CommandOutputBinding:glob "ddecal*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "tec" . sld:default "CS00.*" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "freq" . cwl:source . rdfs:comment "Set weights to this values (0=flagged), by default 1." ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).skymodel_name)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:source . sld:default 20 ; sld:type xsd:int , sld:null . rdfs:label "losoto_plot_B2" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . sld:type cwl:File . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:in , , , , , ; cwl:out , ; cwl:run . sld:default "MODEL_DATA" . sld:default 2e+07 , 1e+09 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "faraday" . sld:default -3.14e+00 , 3.14e+00 . sld:default "initial" . sld:default "diagonal" . a cwl:CommandLineTool ; rdfs:comment "This operation for LoSoTo implement a extend flag procedure.\nIt can work in multi dimensional space and for each datum check if the\n surrounding data are flagged to a certain %, then flag also that datum.\nThe size of the surrounding footprint can be tuned\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('FLAGEXTEND').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "clock" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory , sld:null . rdfs:comment "1- or 2-element array which says the coordinates to plot (2 for 3D plots).\n" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default false . rdfs:label "write_solutions" ; cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . rdfs:label "BLsmooth" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "merge_skymodels*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default true . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Solution table" ; sld:type xsd:string . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "195.3125kHz" ; sld:type xsd:string , sld:null . rdfs:label "concat_logfiles_apply" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . rdfs:label "PolAlign" ; cwl:in , , ; cwl:out , ; cwl:run . sld:default "clock" . rdfs:label "concat_logfiles_dp3" ; cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Max number of independent flagging cycles, by default 5." ; sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:default 4 ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--inmodel2=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "$LINC_DATA_ROOT/skymodels/A-Team.skymodel" ; sld:type cwl:File , xsd:string , sld:null . rdfs:label "prepare_FR" ; cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "ant" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--ylabel" ] ; sld:type xsd:string , sld:null . sld:default false . rdfs:comment "Maximum allowable standard deviation when outlier clipping is done. For phases, this should value\nshould be in radians, for amplitudes in log(amp). If None (or negative), a value of 0.1 rad is\nused for phases and 0.01 for amplitudes.\n" ; sld:type xsd:float , sld:null . rdfs:comment "Number of threads DP3 is allowed to use." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--demix" ; CommandLineBinding:separate true ; CommandLineBinding:shellQuote false ] ; sld:default "False" ; sld:type xsd:string , sld:null . rdfs:comment "Path of parmdb in which the parameters are stored. This can also be an H5Parm file, in that case the filename has to end in '.h5'" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.parmdb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.parmdb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.parmdb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.parmdb=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.parmdb=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . sld:default "polalign_amp_" . rdfs:comment "Controls the accuracy to be reached." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.tolerance=" ; CommandLineBinding:separate false ] ; sld:default 1e-03 ; sld:type xsd:float , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "ant" . sld:default "time" , "freq" . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:comment "Faraday rotation extraction from either a rotation table or a\ncircular phase (of which the operation get the polarisation difference).\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('FARADAY').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:default "sol000/amplitude000" . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:source . cwl:source . sld:default true . rdfs:comment "This sets the number of standard deviations considered when outlier\n clipping is done.\n" ; sld:type xsd:float , sld:null . cwl:source . cwl:source . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:label "DP3.Execute" ; cwl:in , , , , , , , , , , ; cwl:out , , , ; cwl:run . rdfs:comment "Type of the pipeline" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--run_type" ] ; sld:default "calibrator" ; sld:type xsd:string , sld:null . sld:default 0 . cwl:source . rdfs:label "final_flags_join" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.join(','))" . cwl:source . rdfs:label "concat_logfiles_applybeam" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:default "pol" . cwl:source . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default "DELETE COLUMN CIRC_PHASEDIFF_DATA, FR_MODEL_DATA" . sld:default "CORRECTED_DATA" . rdfs:comment "Column name to smooth" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-i" ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).file)" ; cwl:loadContents true ] ; sld:type cwl:File . sld:default false . rdfs:comment "Do not smooth in time" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-t" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . rdfs:comment "Reference antenna, if not set use the first one." ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self+'.skymodel')" . rdfs:comment "Keep history of the export soltabs" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-H" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-H" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-H" ] ; sld:default false ; sld:type xsd:boolean . cwl:source . sld:default "HBA" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "CORRECTED_DATA" . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . sld:default "CIRC_PHASEDIFF_DATA" . sld:default 2e+03 . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; sld:default "sol000" ; sld:type xsd:string . rdfs:comment "Name of the pipeline" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--pipeline" ] ; sld:default "LINC" ; sld:type xsd:string , sld:null . rdfs:comment "If True, skip flagging of international LOFAR stations (only used if\n telescope = 'lofar')\n" ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default "applycal" . rdfs:comment "Solution table" ; sld:type xsd:string . sld:default "ant" . cwl:source . rdfs:label "concat_logfiles_apply" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "PA" ; cwl:in , , , , , , , , , , , ; cwl:out , , , , , , ; cwl:run . rdfs:comment "output table name (same solset)" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "List of model data to be reused from previous (ddecal) step(s). The list should contain the model data names, as set by a previous step" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.reusemodel=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "calibrator" . cwl:outputSource ; sld:type cwl:File . rdfs:label "plot_demix_solutions" ; cwl:in , ; cwl:out , ; cwl:run ; cwl:when "$(inputs.demix)" . sld:default "bandpass.h5" . sld:default "clock" . cwl:source . sld:default "median" . cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:label "H5parm_collector" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type cwl:File . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Output logfile" ; cwl:outputBinding [ CommandOutputBinding:glob "ddecal*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "ddecal*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "ddecal*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "define_parset" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" "input.parset" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "steps = [filter,count,$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')avg]\n#\nmsout.storagemanager = \"Dysco\"\nmsout.storagemanager.databitrate = 0\n#\nfilter.type = filter\nfilter.baseline = $(inputs.filter_baselines)\nfilter.remove = true\n#\nflagedge.type = preflagger\nflagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1]\n#\naoflag.type = aoflagger\naoflag.memoryperc = $(inputs.memoryperc)\naoflag.keepstatistics = false\n#\nflagbaseline.type = preflagger\nflagbaseline.baseline = $(inputs.baselines_to_flag)\n#\nflagelev.type = preflagger\nflagelev.elevation = $(inputs.elevation_to_flag)\n#\nflagamp.type = preflagger\nflagamp.amplmin = $(inputs.min_amplitude_to_flag)\n#\navg.type = average\navg.timeresolution = $(inputs.timeresolution)\navg.freqresolution = $(inputs.freqresolution)\n#\ndemix.type = demixer\ndemix.baseline = $(inputs.process_baselines_cal)\ndemix.demixfreqresolution = $(inputs.demix_freqres)\ndemix.demixtimeresolution = $(inputs.demix_timeres)\ndemix.ignoretarget = False\ndemix.targetsource = $(inputs.target_source)\ndemix.subtractsources = $(inputs.subtract_sources)\ndemix.ntimechunk = $(inputs.ntimechunk)\ndemix.freqstep = 1\ndemix.timestep = 1\ndemix.instrumentmodel = demix_solutions\ndemix.uselbfgssolver = True\ndemix.lbfgs.historysize = $(inputs.lbfgs_historysize)\ndemix.lbfgs.robustdof = $(inputs.lbfgs_robustdof)\ndemix.maxiter = $(inputs.demix_maxiter)\ndemix.lbfgs.solution.range = [-10000,10000]\n" ; cwl:entryname "input.parset" ] ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "DP3.parset" . cwl:source . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "concat_logfiles_beam" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Step size in time for subsequent plotting\n" ; sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . sld:default "sol000/rotation000" . rdfs:comment "Solution interval in timesteps" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solint=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solint=" ; CommandLineBinding:separate false ] ; sld:default 1 ; sld:type xsd:int , sld:null . sld:default "ant" . cwl:in , , ; cwl:out , ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "BLsmooth" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "BLsmooth.py" ) ; cwl:baseCommand ( "BLsmooth.py" ) ; cwl:baseCommand ( "BLsmooth.py" ) ; cwl:baseCommand ( "BLsmooth.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:stderr "BLsmooth.log" . rdfs:comment "Maximum number of iterations" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxiter=" ; CommandLineBinding:separate false ] ; sld:default 50 ; sld:type xsd:int , sld:null . sld:default false . rdfs:comment "Filename of output H5Parm" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.h5parm=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.h5parm=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.h5parm=" ; CommandLineBinding:separate false ] ; sld:default "instrument.h5" ; sld:type xsd:string , sld:null . rdfs:comment "Instead of calculating rms use this value, by default 0 (ignored)." ; sld:type xsd:float , sld:null . sld:default "calibrator" . a cwl:CommandLineTool ; rdfs:label "concatfiles" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:baseCommand ( "bash" "bulk_rename.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nFILE_LIST=(\"\\${@}\")\nFILE_PREFIX=$(inputs.file_prefix)\nFILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix)\ncat \"\\${FILE_LIST[@]}\" > $FILE_PREFIX.$FILE_SUFFIX\n" ; cwl:entryname "bulk_rename.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.onebeamperpatch=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "demix.skymodel=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File . sld:default "sol000/polalign" . sld:default 0 ; sld:type sld:null ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . sld:default "applybeam" . cwl:source . rdfs:comment "Command with respect to the input task" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(inputs.command+\"'\")" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(inputs.command+\"'\")" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(inputs.command+\"'\")" ] ; sld:type xsd:string . cwl:in , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "overwrite output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:default true ; sld:type xsd:boolean . rdfs:comment "Gives an indication on how strong is the ionosphere" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-f" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-f" ] ; sld:default 1e-02 ; sld:type xsd:float , sld:null . sld:default "$LINC_DATA_ROOT/rfistrategies/lofar-hba-wideband.lua" ; sld:type cwl:File , xsd:string , sld:null . sld:default 1 ; sld:type xsd:float , sld:null . sld:default "sol000/phase000" . rdfs:comment "Detect and remove phase wraps, by default True.\n" ; sld:type xsd:boolean , sld:null . sld:default "ant" . sld:type xsd:float , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:float , sld:null . rdfs:label "applybeam" ; cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.missingantennabehavior=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.missingantennabehavior=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.missingantennabehavior=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.missingantennabehavior=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.missingantennabehavior=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "List of model data to be reused from previous (ddecal) step(s). The list should contain the model data names, as set by a previous step" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.reusemodel=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.reusemodel=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.reusemodel=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.autoweight=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:type cwl:Directory . cwl:source . sld:default "Dysco" . sld:default true . cwl:source . sld:default "time" , "freq" . sld:default "applycal" . cwl:source . rdfs:comment "Optional extra data columns to read" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.extradatacolumns=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:default true . cwl:source . sld:default "sol000/phase000" . sld:default "faraday" . sld:default 1e+00 ; sld:type xsd:float , sld:null . rdfs:comment "Fundamental width between samples in axisToRegrid. E.g., \"100kHz\" or \"10s\". If \"\",\nit is calculated from the axisToRegrid values\n" ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:default 17 . cwl:source . sld:default -3.14e+00 , 3.14e+00 . sld:default 500000 , 0 , 100000000000000000000 . cwl:source . rdfs:comment "Type of correction to perform. When using H5Parm, this is for now the name of the soltab; the type will be deduced from the metadata in that soltab, except for full Jones, in which case correction should be 'fulljones'.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.correction=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.correction=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.correction=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.correction=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.correction=" ; CommandLineBinding:separate false ] ; sld:default "gain" ; sld:type xsd:string . cwl:source . sld:default "losoto_PA" . sld:type cwl:File , sld:null . rdfs:comment "Reference antenna, by default None." ; sld:type xsd:string , sld:null . rdfs:comment "Flagged data are replaced with smoothed value and unflagged, by default False." ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "numthreads=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . sld:default "ALTER TABLE" . rdfs:comment "Fitting algorithm: bandpass or resid. Bandpass mode clips amplitudes\n relative to a model bandpass (only LOFAR is currently supported).\nResid mode clips residual phases or log(amplitudes).\n" ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:default "CORRECTED_DATA" . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--min_separation" ] ; sld:type xsd:int , sld:null . rdfs:comment "Window size for the running rms, by default 11." ; sld:type xsd:int , sld:null . sld:type cwl:File . sld:default 5e-01 ; sld:type xsd:float , sld:null . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string . rdfs:label "concat_logfiles_prep_cal" ; cwl:in , ; cwl:out ; cwl:run . sld:default true . rdfs:comment "Save statistics as JSON file" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solveralgorithm=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solveralgorithm=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solveralgorithm=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:source . sld:default "SMOOTHED_DATA" . cwl:source ; sld:default 1 . sld:default 10 ; sld:type xsd:int , sld:null . sld:default 5 . rdfs:comment "Input Measurement Set(s)" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.map(function(directory){ return directory.basename; }).join(','))]" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "scalarphase" . cwl:source . rdfs:comment "Runningmedian or runningpoly or Savitzky-Golay or mean or median (these last two values set all the solutions to the mean/median), by default \"runningmedian\"." ; sld:default "runningmedian" ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] . sld:type xsd:boolean , sld:null . cwl:in , , , , , , ; cwl:out , ; cwl:run . sld:default "polalign" . a cwl:CommandLineTool ; rdfs:comment "This operation for LoSoTo implements a station-flagging procedure. Flags are time-independent.\nWEIGHT: compliant\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('FLAGSTATION').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('FLAGSTATION').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:default "apply_cal_PA" . cwl:source . rdfs:comment "Type of correction to perform. When using H5Parm, this is for now the name of the soltab; the type will be deduced from the metadata in that soltab, except for full Jones, in which case correction should be 'fulljones'.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.type=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applybeam.type=" ; CommandLineBinding:separate false ] ; sld:default "applybeam" ; sld:type xsd:string , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:comment "This operation for LoSoTo implements regridding and linear interpolation of data for an axis.\nWEIGHT: compliant\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "$(get_losoto_config('INTERPOLATE').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . sld:default true ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Dictionary that contains the flagged fraction per station" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . sld:default "ampAFlag_" . a cwl:CommandLineTool ; rdfs:label "H5parm_collector" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.outh5parmname)-parm_collector_output_err.log" ; cwl:stdout "$(inputs.outh5parmname)-parm_collector_output.log" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.usechannelfreq=False" ; CommandLineBinding:separate false ; cwl:valueFrom "$(!self)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "ant" . cwl:source . cwl:source . sld:type xsd:int , sld:null . sld:default "sol000/phase000" . sld:default "applybeam" . rdfs:label "apply_calibrate_fr" ; cwl:in , , , , , , ; cwl:out , , , , ; cwl:run ; cwl:scatter ( ) . sld:default "sol000/clock" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.beammode=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:source . sld:default "pol" . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.basename+\":CIRC_PHASEDIFF_DATA\")" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file_prefix).$(inputs.file_suffix)" ] ; sld:type cwl:File . cwl:source . rdfs:comment "output soltab name for tec3rd offset" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "H5parm_collector" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . rdfs:comment "Make a plot containing antenna coordinates in x,y and in color the value\n to plot, axesInPlot must be [ant].\n" ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "calibrator" . cwl:source . sld:type cwl:Directory , cwl:File . cwl:source . sld:default true . sld:default "sol000/bandpass" . cwl:source . sld:default 20 ; sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "time" , "freq" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solutions" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default -3.14e+00 , 3.14e+00 . rdfs:comment "Solution table" ; sld:default "sol000/rotation000" ; sld:type xsd:string , sld:null . sld:default "predict_cal" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.usechannelfreq=False" ; cwl:valueFrom "$(!self)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default "blsmooth_prep" . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . rdfs:comment "Output h5parm" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; sld:type cwl:File . sld:default 300 . cwl:source . cwl:source . cwl:source . rdfs:comment "Solution table" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "phaseOrig" . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self ? \"True\" : \"False\")" . sld:type cwl:Directory . rdfs:comment "Output data column name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "CORRECTED_DATA" ; sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . sld:default "DATA" . sld:default "FR_MODEL_DATA" . cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "Output MS" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--outms" ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:source . sld:default 0 . sld:default 4 ; sld:type xsd:int , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:default "faraday.h5" . sld:default "sol000/phase000" . sld:default "losoto_bandpass" . sld:default "CasA_Gaussian" , "CygA_Gaussian" , "TauA_Gaussian" , "VirA_Gaussian" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:label "losoto_plot_Pd" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . sld:default "copy" . sld:default 10 ; sld:type xsd:int , sld:null . sld:default "ampBFlag_" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Maximum number of iterations" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxiter=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxiter=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxiter=" ; CommandLineBinding:separate false ] ; sld:default 50 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).demix_maxiter)" ; cwl:loadContents true ] ; sld:type xsd:int . cwl:linkMerge "merge_flattened" ; cwl:source , , . rdfs:label "losoto_plot_P3" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin "$(inputs.max_dp3_threads)" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "DP3_err.log" ; cwl:stdout "DP3.log" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . rdfs:comment "Degrees of the polynomia for the runningpoly or savitzky-golay modes, by default 1." ; sld:type xsd:int , sld:null . rdfs:comment "Comma-separated list of sources to be trusted" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--trusted" ] ; sld:type xsd:string , sld:null . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "specifies a customized strategy\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-strategy" ; CommandLineBinding:separate true ; CommandLineBinding:shellQuote false ] ; sld:default "$LINC_DATA_ROOT/rfistrategies/lofar-default.lua" ; sld:type cwl:File , xsd:string , sld:null . cwl:source . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(\"out_\"+self.basename)" . cwl:source ; cwl:valueFrom "$([self])" . sld:default "calib_cal_bandpass" . cwl:source . rdfs:comment "Re-apply flags to bad values (1 for amp, 0 for other tables), by default False." ; sld:type xsd:boolean , sld:null . sld:default "SMOOTHED_DATA" . cwl:in , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . sld:default true . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . rdfs:comment "Input measurement set and column name" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--inms" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:source . sld:default "ant" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.beammode=" ; CommandLineBinding:separate false ] ; sld:default "default" ; sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "removes all axes with the length of 1" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; sld:default false ; sld:type xsd:boolean . sld:default "calibrator" . rdfs:label "losoto_plot_Pr" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "phaseOrig" . cwl:source . sld:type xsd:int , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . cwl:source ; cwl:valueFrom "$(self ? [\"tec\", \"OrigClock\", \"tec3rd\"] : [\"tec\", \"OrigClock\"])" . rdfs:label "losoto_plot_P3" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , , , , , . rdfs:label "ion" ; cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . sld:default 2 . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "sol000/bandpass" . rdfs:comment "Will skip an ms if it has already been processed by AOFlagger according\nto its HISTORY table.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-skip-flagged" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . sld:default true . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.solveralgorithm=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:comment "Maximum number of iterations during approximating stage" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.maxapproxiter=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . sld:default "CORRECTED_DATA" . cwl:source . sld:default "FR_MODEL_DATA" . sld:default "sol000/phase000" . rdfs:label "concat_logfiles_applybeam" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Soltab to export station flags to. Note: exported flags are not time- or\nfrequency-dependent.\n" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.sourcedb=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File . sld:default true . sld:default "applycal" . sld:default "CORRECTED_DATA" . sld:type xsd:int , sld:null . rdfs:comment "Solution table" ; sld:type xsd:string . sld:default "sol000/amplitude000" . cwl:source . rdfs:comment "Uses an approximation stage in which the phases are constrained with the piece-wise fitter, to solve local minima problems." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approximatetec=True" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approximatetec=True" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.approximatetec=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "sol000/bandpass" . sld:default "blsmooth_bandpass" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).lbfgs_robustdof)" ; cwl:loadContents true ] ; sld:type xsd:float . sld:default "pol" . rdfs:comment "An optional reference frequency (in Hz) for the smoothness constraint" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessreffrequency=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessreffrequency=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.smoothnessreffrequency=" ; CommandLineBinding:separate false ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).lbfgs_historysize)" ; cwl:loadContents true ] ; sld:type xsd:int . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Separate phase solutions into Clock and TEC.\nThe Clock and TEC values are stored in the specified output soltab with type 'clock', 'tec', 'tec3rd'.\n" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--verbose" "$(inputs.input_h5parm.basename)" "parset.config" ) ; cwl:baseCommand ( "losoto" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "astronrd/linc" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_h5parm)" ; cwl:entryname "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "$(get_losoto_config('CLOCKTEC').join('\\n'))" ; cwl:entryname "parset.config" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . cwl:source . rdfs:comment "Controls the accuracy to be reached." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.tolerance=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.tolerance=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "ddecal.tolerance=" ; CommandLineBinding:separate false ] ; sld:default 1e-03 ; sld:type xsd:float , sld:null . sld:default "freq" . rdfs:comment "Filename of output H5Parm" ; cwl:inputBinding [ CommandLineBinding:prefix "ddecal.h5parm=" ; CommandLineBinding:separate false ] ; sld:default "instrument.h5" ; sld:type xsd:string , sld:null . sld:default "bandpass" . cwl:in , , , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:label "get_circ_phasedif" ; cwl:in , ; cwl:out , ; cwl:run . cwl:source . sld:default "CORRECTED_DATA" . rdfs:comment "replace using smoothed value instead of flag bad data? Smooth must be active." ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Output logfile" ; cwl:outputBinding [ CommandOutputBinding:glob "dp3_addcol*.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "dp3_addcol*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . cwl:source . sld:default "[FUSPID].*" ; sld:type xsd:string , sld:null . rdfs:comment "Output sol tab name" ; sld:type xsd:string . rdfs:label "concat_logfiles_applycal" ; cwl:in , ; cwl:out ; cwl:run . cwl:pickValue "first_non_null" ; cwl:source , . rdfs:label "concat_logfiles_calib_cal" ; cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . sld:default true . cwl:outputSource ; sld:type cwl:File . sld:default "MODEL_DATA" . sld:default false . rdfs:comment "Directory or file containing the sky models" ; sld:type cwl:Directory , cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out.json" ; sld:type xsd:string , sld:null . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_h5parm.basename)-losoto*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . sld:default 5e-01 ; sld:type xsd:float , sld:null . sld:default false . sld:default 16 ; sld:type xsd:int , sld:null . rdfs:comment "Will perform the slowest IO but will always work.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-direct-read" ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "sol000/phaseOrig" . sld:default "time" . sld:default "sol000/bandpass" . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).refant)" ; cwl:loadContents true ] ; cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).refant)" ; cwl:loadContents true ] ; cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).refant)" ; cwl:loadContents true ] ; sld:type xsd:string . rdfs:label "concat_logfiles_ion" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Max average residual in radians before flagging datapoint,\nby default 1. If 0: no check.\n" ; sld:type xsd:float , sld:null . rdfs:comment "Whether to plot also flags as red points in 2D plots." ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . rdfs:comment "list of flagged antennas per MS" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] .