@prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix InlineJavascriptRequirement: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix InplaceUpdateRequirement: . @prefix rdf: . @prefix ScatterMethod: . @prefix Dirent: . @prefix cwl: . @prefix ExpressionTool: . cwl:source . rdfs:comment "Input h5parm solutions file" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:default 20000 . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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 xsd:string , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "Ateamclipper" . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "outtype=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "outtype=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "blob" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "AOFlagger" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "aoflag.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.concat_meta_ms)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.concat_additional_ms)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\ndirectories=\\$(ls -d out*)\necho \\${directories}\nmkdir -pv workdir\ncp -r \\${directories} workdir/. && cd workdir\nconcat=out.MS_[0-9*]\neval aoflagger \\${1} \\${2} \\${3} \\${4} \\${5} \\${6} \\${concat}\n" ; cwl:entryname "aoflag.sh" ] ] ; cwl:stderr "aoflag_err.log" ; cwl:stdout "aoflag.log" . rdfs:label "concat_logfiles_dpppconcat" ; cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:default 5e-01 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-temp-dir" ; CommandLineBinding:shellQuote false ] ; sld:default "/tmp/" ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:label "sorttimesintofreqGroups" ; cwl:in , , , , , ; cwl:out , , , ; cwl:run . 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:default "" ; sld:type xsd:string , sld:null . sld:default 8 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Output h5parm name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outh5parm" ] ; sld:default "output.h5" ; sld:type xsd:string . sld:default "target" . cwl:source . cwl:source . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.autoweight=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "time" , "freq" . sld:default 16 ; sld:type xsd:int , sld:null . sld:type xsd:string . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:Directory ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:label "concat_logfiles_clipper_output" ; cwl:in , , ; cwl:out ; cwl:run . sld:default 20 ; sld:type xsd:int , sld:null . rdfs:comment "Number of columns in a multi-table image. By default is automatically\nchosen.\n" ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , , , , . sld:default "" ; sld:type xsd:string , sld:null . rdfs:comment "Comma separated list of (zero-indexed) band ids to process" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-bands" ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . rdfs:label "uvplot" ; cwl:in , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "applyPA.parmdb=$(inputs.solutions.path)" "applybandpass.parmdb=$(inputs.solutions.path)" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "DPPP_err.log" ; cwl:stdout "DPPP.log" . rdfs:comment "Specify proxy server if necessary" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--proxyserver" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "compare_station_list.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nfrom compareStationList import main as compareStationList\n\nmss = sys.argv[1:]\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\nh5parmdb = inputs['h5parmdb']['path']\nsolset_name = inputs['solset_name']\nfilter = inputs['filter']\n\noutput = compareStationList(mss, h5parmdb, solset_name, filter)\n\nfilter_out = output['filter']\ncwl_output = {\"filter_out\": filter_out}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "compare_station_list.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "compareStationList_err.log" ; cwl:stdout "compareStationList.log" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--Ateam_separation_file" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "MS to sort" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:label "concat_logfiles_wsclean" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "DPPP.parset" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--demix True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default true . sld:default true ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:type xsd:int , sld:null . rdfs:comment "Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data." ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "identifyBadAntennas.log" ] ; sld:type cwl:File . rdfs:label "Ateamclipper" ; cwl:in ; cwl:out , , ; cwl:run . sld:type xsd:string . cwl:source . rdfs:label "structure_function" ; cwl:in , , , ; cwl:out , , ; cwl:run . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parm.basename)" ] ; sld:type cwl:File . 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 . cwl:format ; sld:type cwl:File . rdfs:comment "Output data column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . rdfs:comment "Summary File in JSON format" ; cwl:outputBinding [ CommandOutputBinding:glob "*.json" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).filename)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:source . sld:default true . sld:default true . sld:default "CasA_4_patch" , "CygAGG" , "TauAGG" , "VirA_4_patch" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type xsd:string . rdfs:comment "Namebase of the output files" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outbasename" ] ; sld:default "POINTING" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.tolerance=" ; CommandLineBinding:separate false ] ; sld:default 1e-03 ; sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "calibrate_target" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . sld:default 2 . rdfs:label "check_unflagged_fraction" ; cwl:in , ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "wsclean*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "identifyBadAntennas.py" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" "import sys\nimport json\nfrom identifyBadAntennas import main as identifyBadAntennas\n\nms = sys.argv[1]\n\noutput = identifyBadAntennas(ms)\n\nflaggedants = output['flaggedants']\ncwl_output = {\"flaggedants\": flaggedants}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n \n" ) ; cwl:baseCommand ( "python3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "identifyBadAntennas_err.log" ; cwl:stdout "identifyBadAntennas.log" . rdfs:comment "Number of how many files should be grouped together in frequency." ; sld:default 10 ; sld:type xsd:int , sld:null . rdfs:label "concat_logfiles_stationlist" ; cwl:in , ; cwl:out ; cwl:run . rdfs:label "concat_logfiles_identify" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . rdfs:label "h5parm_pointingname" ; cwl:in , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . sld:default "ph_" . sld:default "target" . cwl:outputBinding [ CommandOutputBinding:glob "concat*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . sld:default 10 ; sld:type xsd:int , sld:null . cwl:source . rdfs:label "concat" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run ; cwl:scatter ( ) . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename2)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-maxuvw-m" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "workdir/$(inputs.msout)_[0-9*]\n" ] ; sld:type cwl:Directory . rdfs:comment "will produce verbose output" ; cwl:inputBinding [ cwl:valueFrom "-v" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "workdir/$(inputs.msout)_*_CONCAT\n" ] ; sld:type cwl:Directory . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[avg]" "msin.orderms=False" "avg.type=average" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stderr "average_err.log" ; cwl:stdout "average.log" . a cwl:CommandLineTool ; rdfs:label "define_parset" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "" ; CommandLineBinding:shellQuote false ; cwl:valueFrom "input.parset" ] [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "" ; CommandLineBinding:shellQuote false ; cwl:valueFrom "DPPP.parset" ] ) ; cwl:baseCommand ( "cp" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "steps = [count1,$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')filter,applyPA,applybandpass,$(inputs.apply_clock_correction?'applyclock,':'')$(inputs.apply_beam_correction?'applybeam,':'')$(inputs.apply_rm_correction?'applyRM,':'')$(inputs.apply_tec_correction?'applytec,':'')$(inputs.apply_phase_correction?'applyphase,':'')avg,count2]\n#\nmsout.storagemanager = \"Dysco\"\nmsout.storagemanager.databitrate = 0\n#\ncount1.type = counter\ncount2.type = counter\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#\napplyPA.type = applycal\napplyPA.correction = polalign\napplyPA.solset = calibrator\n#\napplybandpass.type = applycal\napplybandpass.correction = bandpass\napplybandpass.updateweights = $(inputs.updateweights?'True':'False')\napplybandpass.solset = calibrator\n#\napplyclock.type = applycal\napplyclock.correction = clock\napplyclock.solset = calibrator\n#\napplytec.type = applycal\napplytec.correction = tec\napplytec.solset = calibrator\n#\napplyphase.type = applycal\napplyphase.correction = phaseOrig\napplyphase.solset = calibrator\n#\napplyRM.type = applycal\napplyRM.correction = RMextract\napplyRM.solset = target\n#\napplybeam.type = applybeam\napplybeam.usechannelfreq = True\napplybeam.updateweights = $(inputs.updateweights?'True':'False')\napplybeam.invert = True\napplybeam.beammode = element\n#\navg.type = average\navg.timeresolution = $(inputs.timeresolution)\navg.freqresolution = $(inputs.freqresolution)\n#\ndemix.type = demixer\ndemix.baseline = $(inputs.process_baselines_target)\ndemix.demixfreqstep = $(inputs.demix_freqstep)\ndemix.demixtimestep = $(inputs.demix_timestep)\ndemix.ignoretarget = False\ndemix.targetsource = $(inputs.target_source)\ndemix.subtractsources = $(inputs.subtract_sources)\ndemix.ntimechunk = $(inputs.ntimechunk)\ndemix.freqstep = 1\ndemix.timestep = 1\ndemix.instrumentmodel = instrument\n" ; cwl:entryname "input.parset" ] ] . rdfs:comment "Name of the pointing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--pointing" ] ; sld:default "POINTING" ; sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:label "losoto_plot_Pd2" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . sld:default 20 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(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 ] ; 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 . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "List of h5parm files" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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 ] . cwl:source . sld:default true ; sld:type xsd:boolean , 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 . sld:default 20 ; sld:type xsd:int , sld:null . rdfs:label "losoto_plot_P" ; cwl:in , , , , , , , ; cwl:out , , ; cwl:run . rdfs:label "concat_logfiles_solutions" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-niter" ; CommandLineBinding:shellQuote false ] ; sld:default 1000 ; sld:type xsd:int , sld:null . rdfs:label "prefactor_target" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , ; cwl:run . rdfs:comment "Specify proxy server password if necessary" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--proxypass" ] ; sld:type xsd:string , sld:null . sld:default "" ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . rdfs:label "check_Ateam_separation" ; cwl:in , ; cwl:out , , ; cwl:run . sld:default "log" ; sld:type xsd:string , sld:null . sld:default -3.14e+00 , 3.14e+00 . sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "find_sky.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport shutil\nimport os\nimport json\n\nfrom download_skymodel_target import main as download_skymodel_target\n\nmss = sys.argv[1:]\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\n\nSkymodelPath = inputs['SkymodelPath']\nif SkymodelPath is None:\n SkymodelPath = os.getcwd() + \"/target.skymodel\"\nelse:\n SkymodelPath = SkymodelPath[\"path\"]\n\nRadius = inputs['Radius']\nSource = inputs['Source']\nDoDownload = str(inputs['DoDownload'])\n\noutput = download_skymodel_target(mss, SkymodelPath, Radius, DoDownload, Source)\n\nif \"target.skymodel\" not in SkymodelPath:\n shutil.copyfile(SkymodelPath, \"target.skymodel\")\n" ; cwl:entryname "find_sky.py" ] ] ; cwl:requirements [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:stdout "find_skymodel_target.log" . sld:default "" . cwl:outputBinding [ CommandOutputBinding:glob "filenames.json" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "h5parm_pointingname*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "gaincal*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "target" . cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; cwl:outputBinding [ CommandOutputBinding:glob "findRefAnt.log" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source ; sld:default 1 . sld:default 10 ; sld:type xsd:int , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Minimum amount of subbands to concatenate in frequency." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--min_length" ] ; sld:default 50 ; sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . a cwl:CommandLineTool ; rdfs:label "make_sourcedb_ateam" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "makesourcedb" ) ; cwl:baseCommand ( "makesourcedb" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.logname)" . cwl:source . sld:default "ant" . sld:default "sol000" . sld:default "concat" . cwl:source . cwl:source . rdfs:label "apply_gsmcal" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 . rdfs:comment "Filter these antenna string from the processing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--filter" ] ; sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Gives an indication on how strong is the ionosphere" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-f" ] ; sld:default 2e-01 ; sld:type xsd:float , sld:null . cwl:source . sld:default "sol000/phase000" . cwl:source . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "unflagged_fraction.png" ] ; sld:type cwl:File . sld:default true . cwl:linkMerge "merge_flattened" ; cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[filter,avg,count]" "msin.orderms=False" "avg.type=average" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.msin)" ] ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stderr "concat_err.log" ; cwl:stdout "concat.log" . rdfs:comment "Output h5parm" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parmFile.basename)" ] ; sld:type cwl:File . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default -3.14e+00 , 3.14e+00 . cwl:outputBinding [ CommandOutputBinding:glob "average*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "indentify_bad_antennas.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\n\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\nflaggedants = inputs['flaggedants']\nfilter = inputs['filter']\n\n\nflaggedants_list = [ flaggedant.split(',') for flaggedant in flaggedants ]\nif flaggedants_list:\n flagged_antenna_list = set.intersection(*map(set, flaggedants_list))\nelse:\n flagged_antenna_list = set()\n\nfor flagged_antenna in flagged_antenna_list:\n if flagged_antenna != '':\n filter += ';!' + flagged_antenna + '*&&*'\n\ncwl_output = {\"filter\": filter}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "indentify_bad_antennas.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "identifyBadAntennas_err.log" ; cwl:stdout "identifyBadAntennas.log" . cwl:source . sld:default 7e-01 ; sld:type xsd:float , sld:null . cwl:source ; sld:default 1 . cwl:source . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_image_name)" ] ; sld:type cwl:File . rdfs:label "aoflag" ; cwl:in , , , , , ; cwl:out , ; cwl:run . sld:default "results" . sld:default "97.64kHz" ; sld:type xsd:string , sld:null . cwl:source . rdfs:label "get_targetname" ; cwl:in ; cwl:out , ; cwl:run . sld:default 10000 . sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self+'000')" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applyRM.parmdb=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.solutions.path)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default true . 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:default "prep" . cwl:source . rdfs:comment "Antenna string to be processed" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--bad_antennas" ] ; sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.maxiter=" ; CommandLineBinding:separate false ] ; sld:default 50 ; sld:type xsd:int , sld:null . rdfs:label "concat_logfiles_unflagged" ; cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-mgain" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "target.skymodel" ] ; sld:type cwl:File , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "SMOOTHED_DATA" . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "structure_function" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "getStructure_from_phases.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "structure_function_err.log" ; cwl:stdout "structure_function.log" . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Reference antenna used" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--refant" ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Title of the plots" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--title" ; CommandLineBinding:shellQuote false ] ; sld:default "uv-coverage" ; sld:type xsd:string , sld:null . sld:default "ant" . sld:default "DATA" . cwl:source . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name)" ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.image_name)-MFS-image.fits" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data." ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "wsclean" ; cwl:in , , , , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . sld:default 5 . cwl:linkMerge "merge_flattened" ; cwl:source ; cwl:valueFrom "$(self.nameroot+'_wsclean.ms')" . sld:type cwl:Directory , cwl:File . cwl:source . cwl:source . rdfs:label "save_inspection" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:default "CODG" ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default "CS00.*" ; sld:type xsd:string , sld:null . sld:default "inspection" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; cwl:outputBinding [ CommandOutputBinding:glob "parset.config" ] ; sld:type cwl:File . rdfs:comment "If true performs smoothing" ; cwl:inputBinding [ CommandLineBinding:prefix "-S" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self ? 'True': 'False')" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "check_unflagged_fraction*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File , xsd:string , sld:null . cwl:source . rdfs:comment "List of h5parm files" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.sourcedb=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File . cwl:source . cwl:source ; sld:default false . cwl:source . sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . cwl:source . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.onebeamperpatch=True" ; CommandLineBinding:separate false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-auto-threshold" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . sld:default true . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-parallel-gridding" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default 8e-01 . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "sort_times_into_freqGroups.log" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:source . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . rdfs:comment "Will select either memory or direct mode based on available memory (default).\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-auto-read" ] ; sld:type xsd:boolean , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:outputSource ; sld:type cwl:Directory . sld:default 10 ; sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Use Log=’XYZ’ to set which axes to put in Log.\n" ; sld:type xsd:string , sld:null . 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:source . sld:default 30 ; sld:type xsd:int , sld:null . sld:default "ant" . sld:default "RMextract" . sld:default true . cwl:source . rdfs:comment "Input calibration solutions of the reference h5parm file" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--refsolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default "ant" . cwl:source . rdfs:comment "Filter these baselines for the comparison" ; sld:default "*&" ; sld:type xsd:string , sld:null . sld:type xsd:string . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.join(','))" . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "sort_times.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nfrom sort_times_into_freqGroups import main as sort_times_into_freqGroups\n\nmss = sys.argv[1:]\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\n\nnumbands = inputs['numbands']\nstepname = inputs['stepname']\nNDPPPfill = inputs['NDPPPfill']\nmergeLastGroup = inputs['mergeLastGroup']\ntruncateLastSBs = inputs['truncateLastSBs']\nfirstSB = inputs['firstSB']\n\noutput = sort_times_into_freqGroups(mss, numbands, NDPPPfill, stepname, mergeLastGroup, truncateLastSBs, firstSB)\n\nfilenames = output['filenames']\ngroupnames = output['groupnames']\ntotal_bandwidth = output['total_bandwidth']\n\ncwl_output = {}\ncwl_output['groupnames'] = groupnames\ncwl_output['total_bandwidth'] = total_bandwidth\n\nwith open('./filenames.json', 'w') as fp:\n json.dump(filenames, fp)\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "sort_times.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "sort_times_into_freqGroups_err.log" ; cwl:stdout "sort_times_into_freqGroups.log" . rdfs:comment "removes all axes with the length of 1" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; sld:default false ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "." . cwl:source ; sld:default "*" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applyclock.parmdb=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.solutions.path)" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default true . cwl:source ; sld:default 20 . rdfs:comment "Unwrap phases." ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default 4 . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "avg.timeresolution=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default 1 ; sld:type xsd:int , sld:null . rdfs:label "initial_flags_join" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:label "concat_logfiles_structure" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).filter_out)" ; cwl:loadContents true ] ; sld:type xsd:string . sld:default "identifyBadAntennas" . sld:default false . rdfs:comment "Model data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.modelcolumn=" ; CommandLineBinding:separate false ] ; sld:default "MODEL_DATA" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count2.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$(Math.round(self/1000000))" . sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-no-update-model-required" ; CommandLineBinding:shellQuote false ] ; sld:default true ; sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "h5parm_cat" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(inputs.input_file.basename)" ] ) ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.input_file)" ] ] ; cwl:stderr "h5parm_collector_output_err.log" ; cwl:stdout "h5parm_collector_output.log" . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default "target" . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.writefullresflag=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . rdfs:label "losoto_plot_RM" ; cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solutions" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "ms_concat" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "ms_concat.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\ndirectories=\\$(ls -d out_*)\n#echo \\${directories}\nmkdir -pv workdir\ncp -r \\${directories} workdir/. && cd workdir\nconcat_MS.py \\${1} \\${2} \\${3} \\${4} \\${directories} \\${5}\n" ; cwl:entryname "ms_concat.sh" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InplaceUpdateRequirement ; InplaceUpdateRequirement:inplaceUpdate true ] ; cwl:stderr "ms_concat_err.log" ; cwl:stdout "ms_concat.log" . sld:type cwl:File , xsd:string , sld:null . sld:type xsd:int , sld:null . sld:default true . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . rdfs:comment "Whether to plot also flags as red points in 2D plots." ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "Dysco" . rdfs:comment "Output MS" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . sld:type cwl:Directory , cwl:File . sld:default "time" , "freq" . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . sld:default 16 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Name of the H5parm solset" ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:source . 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 10 ; sld:type xsd:int , sld:null . rdfs:label "merge_array_files" ; cwl:in ; cwl:out ; cwl:run . sld:default "final" . a cwl:ExpressionTool ; rdfs:label "merge_array_files" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var out_file = []\n for(var i=0; i ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:default "RMextract" . sld:default 4 ; sld:type xsd:int , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , , . sld:default "target.sourcedb" . rdfs:comment "removes all axes with the length of 1" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-q" ] ; sld:default false ; sld:type xsd:boolean . rdfs:label "concat_logfiles_prep_target" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "ms_concat.log" ] ; sld:type cwl:File . cwl:source . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "plot_Ateamclipper" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "plot_Ateamclipper.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , ; cwl:outputs . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "flagged_fraction_antenna.json" ] ; cwl:outputBinding [ CommandOutputBinding:glob "flagged_fraction_antenna.json" ] ; 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 . cwl:source . cwl:source . sld:default 16 ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:string , sld:null . rdfs:comment "Input data Column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.datacolumn=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "DATA" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "filter_predict*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-j" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . rdfs:comment "verbose output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; sld:default true ; sld:type xsd:boolean . sld:default 16 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "in=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "in=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "$PREFACTOR_DATA_ROOT/skymodels/Ateam_LBA_CC.skymodel" ; sld:type cwl:File , xsd:string , sld:null . rdfs:label "concat_logfiles_clipper" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . rdfs:label "filter_ms_group" ; cwl:in , , ; cwl:out , ; cwl:run . sld:default "initial" . sld:default 50 . rdfs:comment "MS to compare with" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:symbols , , , , , , , ; sld:type sld:enum . sld:type cwl:File . sld:default "DATA" . cwl:source . sld:default 20 ; sld:type xsd:int , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "structure_function*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . sld:type cwl:File . sld:default 2 . rdfs:comment "MS to compare with" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "predict_targ" . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "compareStationList*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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: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: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: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: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: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: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: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: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: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:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "avg.freqstep=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default 1 ; sld:type xsd:int , sld:null . sld:default true . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:default true . rdfs:comment "Specify proxy user name if necessary" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--proxyuser" ] ; sld:type xsd:string , sld:null . rdfs:label "check_filtered_MS_array" ; cwl:in ; cwl:out ; cwl:run . sld:default 16 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Filter these baselines for the comparison" ; sld:default "*&" ; sld:type xsd:string , sld:null . cwl:source . sld:default 0 . sld:default "phase" ; sld:type xsd:string , sld:null . sld:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:default "make_sourcedb_ateam.log" . cwl:source . cwl:source . rdfs:comment "Input measurement set" ; sld:type cwl:Directory . cwl:source . cwl:source , ; cwl:valueFrom "$(self.join(''))" . cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File ; sld:type [ sld:items cwl:Directory , cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory , cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory , cwl:File ; sld:type sld:array ] . rdfs:comment "Make a plot containing antenna coordinates in x,y and in color the value\n to plot, axesInPlot must be [ant].\n" ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:label "concat_logfiles_gaincal" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "ph_poldif_" . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source ; sld:default 10 . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flaggedants)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:source . 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 cwl:File , sld:null . sld:default "gaincal" . cwl:source , ; cwl:valueFrom "$(self.join(''))" . cwl:outputBinding [ CommandOutputBinding:glob "get_targetname*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "apply_gsmcal" . a cwl:Workflow ; rdfs:label "ndppp_prep_targ" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).targetName)" ; cwl:loadContents true ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "format=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "format=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "\"<\"" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source ; cwl:valueFrom "$(self.nameroot+'_pre-cal.ms')" . sld:default "DATA" . cwl:source . cwl:source . cwl:source . sld:type cwl:File . sld:default false ; sld:type xsd:boolean , sld:null . sld:type cwl:File . rdfs:comment "The type of calibration that needs to be performed.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.caltype=" ; CommandLineBinding:separate false ] ; sld:type . rdfs:comment "MS to check" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:Directory . sld:default 1500 . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Download a new skymodel if given path is empty" ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default "CasA_4_patch" , "CygAGG" , "TauAGG" , "VirA_4_patch" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "pol" . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:outputSource ; sld:type xsd:string . rdfs:comment "If set, then reference the grouping of files to this station-subband. As if a file with this station-subband would be included in the input files." ; sld:type xsd:int , sld:null . sld:default 16 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "gaincal" . rdfs:comment "Comma separated list of (zero-indexed) field ids to process" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-fields" ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "predict_targ" . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.solset=" ; CommandLineBinding:separate false ] ; sld:default "sol000" ; sld:type xsd:string . rdfs:label "concat_logfiles_losoto" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default "ph_" . sld:default "" . sld:default -3.14e+00 , 3.14e+00 . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "make_sourcedb.log" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "msout.overwrite=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "File containing or putting the skymodel" ; sld:type cwl:File , sld:null . cwl:source . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "HBA_target" ; 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:MultipleInputFeatureRequirement ] . cwl:source . sld:default 10 ; sld:type xsd:int , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default true . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "CODG" ; sld:type xsd:string , sld:null . sld:default 10 ; sld:type xsd:int , sld:null . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "plot_unflagged" ; cwl:in , ; cwl:out , ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "count2.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out2.json" ; sld:type xsd:string , sld:null . rdfs:comment "Do not backup the old WEIGHT_SPECTRUM in WEIGHT_SPECTRUM_ORIG" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-b" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "aoflag.log" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . rdfs:comment "overwrite output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:default true ; sld:type xsd:boolean . sld:default 5e-01 ; sld:type xsd:float , sld:null . rdfs:comment "MS to compare with" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:Directory . cwl:source . rdfs:comment "Input Solution Set" ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "uvplot" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "plot_uvcov.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stderr "uvplot_err.log" ; cwl:stdout "uvplot.log" . cwl:source . rdfs:label "make_sourcedb_target" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:label "concat_logfiles_blsmooth" ; cwl:in , ; cwl:out ; cwl:run . sld:default "sol000/phase000" . cwl:source . sld:default "phase" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source ; cwl:valueFrom "$(self)_uv-coverage.png" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . 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 xsd:string . sld:default "" . cwl:source . rdfs:label "merge_array" ; cwl:in ; cwl:out ; cwl:run . rdfs:comment "Name of the soltab" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--soltab" ] ; sld:default "phase000" ; sld:type xsd:string , sld:null . sld:default true . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--demix_sources" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self)" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . sld:default "DATA" . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self+'_summary')" . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "--removed_bands" ; CommandLineBinding:separate true ; cwl:valueFrom "$(self)" ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . cwl:source . rdfs:label "ndppp_prep_target" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , ; cwl:run ; cwl:scatter ( ) . rdfs:comment "h5parm output" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.h5parm.basename)" ] ; sld:type cwl:File . cwl:source ; sld:default false . sld:type xsd:string , sld:null . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--min_separation" ] ; sld:type xsd:int , sld:null . sld:default "losoto_gsmcal" . rdfs:comment "Reads uvw values (some exotic strategies require these)" ; cwl:inputBinding [ CommandLineBinding:prefix "-uvw" ] ; sld:type cwl:File , sld:null . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:source . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:float ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count1.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:label "summary" ; cwl:in , , , , , , , , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Plot of the uv-coverage" ; cwl:outputBinding [ CommandOutputBinding:glob "*$(inputs.output_name.split('.').pop())" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Specify proxy type if necessary" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--proxytype" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applytec.parmdb=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.solutions.path)" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "createh5parm*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:linkMerge "merge_flattened" ; cwl:source , , , , . rdfs:comment "Join all SPWs together in frequency direction before flagging" ; cwl:inputBinding [ CommandLineBinding:prefix "-combine-spws" ] ; sld:type xsd:boolean , sld:null . rdfs:label "concat_logfiles_dpppconcat" ; cwl:in , ; cwl:out ; cwl:run . sld:default "sol000/phase000" . rdfs:comment "Input calibration solutions" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory . sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.propagatesolutions=True" ; CommandLineBinding:separate false ] ; sld:default true ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "h5parm_pointingname" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "h5parm_pointingname.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parmFile)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "h5parm_pointingname_err.log" ; cwl:stdout "h5parm_pointingname.log" . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).filter)" ; cwl:loadContents true ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "plot_unflagged" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" "import sys\nimport os\n\nfrom plot_unflagged_fraction import main as plot_unflagged_fraction\n\ncenter = int((len(sys.argv) - 1) / 2 + 1)\n\nmss = sys.argv[1:center]\nunflagged_fraction = sys.argv[center:]\n\noutput = plot_unflagged_fraction(ms_list = mss, frac_list = unflagged_fraction, outfile = os.getcwd() + '/unflagged_fraction.png')\n" ) ; cwl:baseCommand ( "python3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "plot_unflagged_fraction_err.log" ; cwl:stdout "plot_unflagged_fraction.log" . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . rdfs:comment "Source of the skymodel" ; sld:default "TGSS" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-parallel-reordering" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).groupnames)" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "overrides the number of threads specified in the strategy\n(default: one thread for each CPU core)\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-j" ] ; sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . rdfs:comment "Output h5parm" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_file.basename)" ] ; sld:type cwl:File . rdfs:comment "IONEX Prefix" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--prefix" ] ; sld:default "CODG" ; sld:type xsd:string , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "DPPP*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 8 ; sld:type xsd:int , sld:null . cwl:source , ; cwl:valueFrom "$(self.join(''))" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-size" ; CommandLineBinding:shellQuote false ] ; sld:default 2500 ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . rdfs:comment "Set bandpass correction file for any 'Apply passband' action" ; cwl:inputBinding [ CommandLineBinding:prefix "bandpass" ] ; sld:type cwl:File , sld:null . sld:default "wsclean" . sld:default "losoto_gsmcal" . cwl:source . a cwl:Workflow ; rdfs:label "gsmcal" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).selected_ms)" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default 1e-30 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; sld:type cwl:Directory , cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "filter.remove=True" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applyphase.parmdb=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.solutions.path)" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "97.64kHz" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-parallel-deconvolution" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . cwl:source . rdfs:label "concat_logfiles_calib" ; cwl:in , ; cwl:out ; cwl:run . sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "out=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(inputs.output_file_name)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "out=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(inputs.output_file_name)" ] ; sld:default "Ateam.sourcedb" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "losoto_plot_Pd" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . sld:type xsd:int , sld:null . rdfs:comment "Name of the output image" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--output" ; CommandLineBinding:shellQuote false ] ; sld:default "uv-coverage.png" ; sld:type xsd:string , sld:null . rdfs:comment "Output Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "." ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "add_missing_stations" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "add_missing_stations.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parm)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "add_missing_stations_err.log" ; cwl:stdout "add_missing_stations.log" . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true ; sld:type xsd:boolean , sld:null . sld:default 7e-01 ; sld:type xsd:float , sld:null . sld:default "CODG" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[filter,predict,count]" "predict.beammode=array_factor" "predict.usechannelfreq=False" "msout=." ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "filter_predict_err.log" ; cwl:stdout "filter_predict.log" . sld:default 5 . sld:type xsd:string , sld:null . cwl:source ; sld:default true . sld:default 0 . rdfs:comment "float parameter describing how much of Earth rotation is taken in to account in interpolation of the IONEX files. 1.0 means time interpolation assumes ionosphere rotates in opposite direction of the Earth" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-e" ] ; sld:default 0e+00 ; sld:type xsd:float , sld:null . sld:default "ndppp_prep_targ" . cwl:source . a cwl:CommandLineTool ; rdfs:label "WSClean" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "wsclean" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.msin)" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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 "wsclean_err.log" ; cwl:stdout "wsclean.log" . sld:default "DATA" . a cwl:CommandLineTool ; rdfs:label "CollectFiles" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bash" "collect_files.sh" ) ; cwl:baseCommand ( "bash" "collect_files.sh" ) ; cwl:baseCommand ( "bash" "collect_files.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nBASE_DIR=\"$(inputs.start_directory === null ? \"\" : inputs.start_directory.basename)\"\nSUB_DIR=\"$(inputs.sub_directory_name)\"\nif [ -z \"$BASE_DIR\" ]\nthen\nOUTPUT_PATH=$SUB_DIR\nelse\nOUTPUT_PATH=$BASE_DIR/$SUB_DIR\nfi\necho $OUTPUT_PATH\nmkdir -p $OUTPUT_PATH\ncp -rL $* $OUTPUT_PATH\n" ; cwl:entryname "collect_files.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nBASE_DIR=\"$(inputs.start_directory === null ? \"\" : inputs.start_directory.basename)\"\nSUB_DIR=\"$(inputs.sub_directory_name)\"\nif [ -z \"$BASE_DIR\" ]\nthen\nOUTPUT_PATH=$SUB_DIR\nelse\nOUTPUT_PATH=$BASE_DIR/$SUB_DIR\nfi\necho $OUTPUT_PATH\nmkdir -p $OUTPUT_PATH\ncp -rL $* $OUTPUT_PATH\n" ; cwl:entryname "collect_files.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "#!/bin/bash\nset -e\nBASE_DIR=\"$(inputs.start_directory === null ? \"\" : inputs.start_directory.basename)\"\nSUB_DIR=\"$(inputs.sub_directory_name)\"\nif [ -z \"$BASE_DIR\" ]\nthen\nOUTPUT_PATH=$SUB_DIR\nelse\nOUTPUT_PATH=$BASE_DIR/$SUB_DIR\nfi\necho $OUTPUT_PATH\nmkdir -p $OUTPUT_PATH\ncp -rL $* $OUTPUT_PATH\n" ; cwl:entryname "collect_files.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . sld:default true . sld:default "calibrator" . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Save the newly computed WEIGHT_SPECTRUM, this action permanently modify the MS!" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-w" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Input measurement set" ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Ateamclipper" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "Ateamclipper.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InlineJavascriptRequirement ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:inputs ; cwl:outputs , , ; cwl:stdout "Ateamclipper.log" . rdfs:comment "List of h5parm files" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . sld:default "phaseonly" . cwl:source . sld:default "dppp" . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "Ateamclipper.png" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.parmdb=" ; CommandLineBinding:separate false ] ; sld:default "instrument.h5" ; sld:type xsd:string , sld:null . sld:default "TGSS" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name==\".\"?inputs.msin.basename:inputs.msout_name)" ] ; sld:type cwl:Directory . rdfs:comment "If WEIGHT_SPECTRUM_ORIG exists then restore it before smoothing" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-r" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default 16 ; sld:type xsd:int , sld:null . sld:default "compareStationList" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:type xsd:string . cwl:source . sld:default ".dpppconcat" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "selected_ms.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents))" ; cwl:loadContents true ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.missingdata=True" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:type xsd:boolean , sld:null . sld:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 2 ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(concatenate_path_wsclean(self))" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:default 1 . rdfs:label "prep" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , ; cwl:run . sld:default 30 ; sld:type xsd:int , sld:null . sld:default 4 ; sld:type xsd:int , sld:null . sld:type xsd:string , sld:null . rdfs:comment "solset in which IONEX solution are put" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solsetName" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "pol" . cwl:source ; cwl:valueFrom "$(Math.round((self+1)/4))" . rdfs:comment "Output MS" ; cwl:outputBinding [ CommandOutputBinding:glob "workdir/out_*" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source , ; cwl:valueFrom "$(self.join(''))" . cwl:outputBinding [ CommandOutputBinding:glob "Ateamclipper.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File , sld:null . rdfs:comment "Output plot" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outbasename+'_structure.png')" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "H5parm_collector" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "H5parm_collector.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.outh5parmname)-parm_collector_output_err.log" ; cwl:stdout "$(inputs.outh5parmname)-parm_collector_output.log" . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.usebeammodel=true" ; CommandLineBinding:separate false ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default 5 . sld:default "DATA" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin.baseline=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote true ] ; sld:default "*" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . sld:default "briggs -0.5" . sld:default "ant" . a cwl:Workflow ; rdfs:label "prefactor_target" ; 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:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-join-channels" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.overwrite=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:comment "Will skip an ms if it has already been processed by AOFlagger according\nto its HISTORY table.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-skip-flagged" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "BLsmooth" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "BLsmooth.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "BLsmooth.log" . sld:default 5e-01 ; sld:type xsd:float , sld:null . sld:default "Ateamclipper" . rdfs:label "calibrate_target" ; cwl:in , , , ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) . sld:type cwl:File , sld:null . 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:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:InlineJavascriptRequirement ] ; cwl:inputs , , ; cwl:outputs , , ; cwl:stdout "Ateam_separation.log" . rdfs:label "concat_logfiles_RMextract" ; cwl:in , ; cwl:out ; cwl:run . rdfs:label "merge_array_files" ; cwl:in ; cwl:out ; cwl:run . rdfs:comment "List of MS for UV-plotting" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:shellQuote false ] ; sld:type cwl:Directory ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-weight" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:comment "Type of the pipeline" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--run_type" ] ; sld:default "calibrator" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "Ateam_separation.log" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . sld:default 20 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "avg.timestep=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default 1 ; sld:type xsd:int , sld:null . cwl:source . rdfs:label "concat_logfiles_clipper_output" ; cwl:in ; cwl:out ; cwl:run . rdfs:comment "IONEX path" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--path" ] ; sld:default "./" ; sld:type xsd:string , sld:null . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "Dysco" . cwl:source . sld:default "CasA_4_patch" , "CygAGG" , "TauAGG" , "VirA_4_patch" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . sld:default 1e-30 ; sld:type xsd:float , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , , , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . rdfs:label "concat_logfiles_predict" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "demix.skymodel=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File . rdfs:comment "Prefix to add before the self-generated filename.\n" ; sld:default "losoto.plot." ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "count1.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out1.json" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.sourcedb=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , cwl:File . rdfs:comment "Input solution table" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--soltab_in" ] ; sld:default "phase000" ; sld:type xsd:string , sld:null . rdfs:comment "Filter these baselines for the comparison" ; sld:default "*&" ; sld:type xsd:string , sld:null . rdfs:label "concat_logfiles_uvplot" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "timestep in seconds" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-t" ] ; sld:default 3e+02 ; sld:type xsd:float , sld:null . sld:default true . sld:default "ftp://ftp.aiub.unibe.ch/CODE/" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-scale" ; CommandLineBinding:shellQuote false ] ; sld:default "36asec" ; sld:type xsd:string , sld:null . rdfs:comment "External H5parm from which the full list of antennas is used from." ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--refh5" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "filter.blrange=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default "97.64kHz" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory . cwl:source ; cwl:valueFrom "$(\"out_\"+self.basename)" . cwl:in , , , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "Will reorder the measurement set before starting, which is normally\nfaster but requires free disk space to reorder the data to.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-indirect-read" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--outsolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . cwl:source . sld:default "0deg..15deg" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:comment "Output h5parm name" ; sld:default "output.h5" ; sld:type cwl:File . sld:default true ; sld:type xsd:boolean , sld:null . sld:default "time" . sld:default 16 ; sld:type xsd:int , sld:null . cwl:source ; sld:default true . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "createRMh5parm" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "createRMh5parm.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.h5parm)" ] ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:stderr "createh5parm_err.log" ; cwl:stdout "createh5parm.log" . 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: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 ] . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ] ; sld:default "" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.beammode=" ; CommandLineBinding:separate false ] ; sld:default "array_factor" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . 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 "Will read the entire measurement set in memory. This is the fastest,\nbut requires much memory.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-memory-read" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "filter.baseline=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(self)" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type xsd:int . rdfs:comment "Filename of output H5Parm (to be read by e.g. losoto)" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name_h5parm)" ] ; sld:type cwl:File . rdfs:comment "Name of output MS" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "." ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).unflagged_fraction)" ; cwl:loadContents true ] ; sld:type xsd:float . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:label "average" ; cwl:in , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:default "txt" . rdfs:comment "Output column" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-o" ] ; sld:default "SMOOTHED_DATA" ; sld:type xsd:string , sld:null . cwl:source . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default 2500 . sld:type cwl:Directory . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Only use this fraction of the available memory for deriving the amount\nof data to be concatenated.\n" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--overhead" ] ; sld:default 8e-01 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type xsd:string . 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: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 "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; 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 "$(inputs.input_h5parm.basename)" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(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 $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ; cwl:listing [ cwl:entry "$(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 "$(get_losoto_config('PLOT').join('\\n'))" ; cwl:entryname "parset.config" ] ; cwl:listing [ cwl:entry "#!/bin/bash\nset -e\nINPUT_H5PARM=$(inputs.input_h5parm.basename)\nDO_PLOTS=$(inputs.execute)\nif [ \"$DO_PLOTS\" = \"true\" ]; then\n losoto --verbose $INPUT_H5PARM parset.config\nelse\n echo Skipped plotting 3rd order tec solutions\nfi\n" ; cwl:entryname "run_losoto_plot.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ; InlineJavascriptRequirement:expressionLib "function get_losoto_config(step_name) {\n var par = ['soltab = ' + inputs.soltab]\n if (inputs.ncpu !== null && inputs.ncpu !== undefined) par.push('ncpu='+inputs.ncpu);\n par.push(\"[\" + step_name + \"]\")\n par.push('operation=' + step_name)\n for(var field_name in inputs){\n if(field_name === 'input_h5parm' ||\n field_name === 'soltab' ||\n field_name === 'ncpu' || \n field_name === 'execute') continue;\n\n if(inputs[field_name] === null ||\n inputs[field_name] === 'null') continue;\n \n if(inputs[field_name][\"class\"] !== undefined &&\n (inputs[field_name][\"class\"] ===\"Directory\" ||\n inputs[field_name][\"class\"] ===\"File\")){\n par.push(field_name+'='+inputs[field_name].path)\n } else {\n par.push(field_name+'='+inputs[field_name])\n }\n }\n return par\n}\n\nfunction concatenate_path(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return '[' + object_list.join(',') + ']'\n \n}\n\nfunction concatenate_path_wsclean(object_list){\n object_list.forEach(function (x, index, arr) {arr[index] = x.path;});\n return object_list.join(' ')\n \n}" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(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:stderr "$(inputs.input_h5parm.basename)-losoto_err.log" ; cwl:stdout "$(inputs.input_h5parm.basename)-losoto.log" . rdfs:comment "Keep history of the export soltabs" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-H" ] ; sld:default false ; sld:type xsd:boolean . rdfs:label "save_results" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Output h5parm" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:Directory . rdfs:label "find_skymodel_target" ; cwl:in , , , , ; cwl:out , ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "ph_poldif" . cwl:source . sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "h5parm_collector_output*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "find_skymodel_target.log" ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "15asec" . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$(self.join(','))" . rdfs:comment "Input Measurement Set" ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "createRMh5parm" ; cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source ; cwl:valueFrom "$(self.join(','))" . rdfs:comment "Input Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ] ; sld:type cwl:Directory , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:default 0 . cwl:inputBinding [ CommandLineBinding:prefix "msout.writefullresflag=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name==\".\"?inputs.msin.basename:inputs.msout_name)" ] ; sld:type cwl:Directory . rdfs:comment "Add dummy file-names for missing frequencies, so that NDPPP can fill the data with flagged dummy data." ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File , sld:null . sld:default "Dysco" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "applycal.updateweights=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ] ; sld:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.overwrite=True" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Tabs to plot" ; sld:type xsd:string . sld:default 4 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--outputimage" ] ; sld:default "Ateam_separation.png" ; sld:type xsd:string , sld:null . rdfs:comment "Smooth only amplitudes" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-a" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "H5parm_collector" ; cwl:in , , , ; cwl:out , ; cwl:run . sld:default "uvplot" . sld:default 16 ; sld:type xsd:int , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . rdfs:comment "Fraction of flagged data in a MS to be acceptable" ; sld:default 5e-01 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:Directory . sld:default 0 . sld:default "blsmooth_target" . 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 "$(inputs.prefix)*.png" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--structure_file" ] ; sld:default false ; sld:type xsd:boolean , cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:label "identifybadantennas_join" ; cwl:in , ; cwl:out , ; cwl:run . sld:default "CasA_4_patch" , "CygAGG" , "TauAGG" , "VirA_4_patch" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:label "Ateam_flags_join" ; cwl:in , , ; cwl:out ; cwl:run . sld:default 10 ; sld:type xsd:int , sld:null . cwl:source . sld:default 10 ; sld:type xsd:int , sld:null . sld:default "" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.image_name)-MFS-dirty.fits" ] ; sld:type cwl:File . sld:default 5 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Make a movie summing up all the produced plots.\n" ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "findRefAnt_join" ; cwl:in , ; cwl:out , ; cwl:run . sld:default "dpppconcat" . cwl:outputBinding [ CommandOutputBinding:glob "L*.dpppconcat" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default 50 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type [ sld:items [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type sld:array ] . 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.start_directory === null ? inputs.sub_directory_name: inputs.start_directory.basename)\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.start_directory === null ? inputs.sub_directory_name: inputs.start_directory.basename)\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.start_directory === null ? inputs.sub_directory_name: inputs.start_directory.basename)\n" ] ; sld:type cwl:Directory . rdfs:label "identifybadantennas" ; cwl:in ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type xsd:string . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name==\".\" ? inputs.msin.basename : inputs.msout_name)" ] ; sld:type cwl:Directory . sld:type cwl:File , xsd:string , sld:null . sld:default 16 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.onebeamperpatch=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Name of the pipeline" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--pipeline" ] ; sld:default "prefactor" ; sld:type xsd:string , sld:null . rdfs:comment "Input measurement set" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:Directory ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "target" . rdfs:comment "Will perform the slowest IO but will always work.\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-direct-read" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "filter_ms_group" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 0 ; cwl:valueFrom "filter_ms_group.py" ] ) ; cwl:baseCommand ( "python3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.measurement_sets)" ] ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nimport os\n\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\ngroup_id = inputs['group_id']\njson_file = sys.argv[1]\nms_list = sys.argv[2:]\n\nms_by_name = { ms.split(os.path.sep)[-1]:\n {'class':'Directory', 'path': ms} for ms in ms_list}\n\noutput_file = 'selected_ms.json'\n\nwith open(json_file, 'r') as f_stream:\n selected_ms = json.load(f_stream)[group_id]\n\nselected_ms = [os.path.basename(ms_name) for ms_name in selected_ms]\ncwl_output = {'selected_ms': selected_ms}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n\nselected_ms = [ms_by_name[ms_name] for ms_name in selected_ms if ms_name != 'dummy.ms']\n\n\nwith open(output_file, 'w') as f_stream:\n json.dump(selected_ms, f_stream)\n" ; cwl:entryname "filter_ms_group.py" ] ] ; cwl:stderr "filter_ms_by_group_err.log" ; cwl:stdout "filter_ms_by_group.log" . sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "concat_logfiles_summary" ; cwl:in , ; cwl:out ; cwl:run . sld:default "DATA" . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-nmiter" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "filter.remove=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:default "target/RMextract" . cwl:outputBinding [ CommandOutputBinding:glob "out.json" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).total_bandwidth)" ; cwl:loadContents true ] ; sld:type xsd:int . rdfs:label "finalize" ; cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , ; cwl:run . sld:default "sol000/phase000" . rdfs:comment "H5parm database to compare with" ; sld:type cwl:File . sld:default "CS00.*" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "identifyBadAntennas.log" ] ; sld:type cwl:File . sld:default "target" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.usechannelfreq=True" ; CommandLineBinding:separate false ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Number of cpus, by default all available." ; sld:type xsd:int , sld:null . rdfs:label "concat_logfiles_dppp" ; 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 "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:stderr "summary_err.log" ; cwl:stdout "summary.log" . cwl:source . cwl:source . sld:default "target" . sld:type xsd:string , sld:null . cwl:source ; sld:default false . cwl:outputSource ; sld:type xsd:string . sld:default 5 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-multiscale" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . 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 . rdfs:label "DP3.Execute" ; cwl:in , , , , , , , , , , ; cwl:out , , , ; cwl:run . cwl:source . sld:default "" ; sld:type xsd:string , sld:null . 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 ] ; sld:default "gain" ; sld:type xsd:string . sld:default false . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "applycal_$(inputs.correction).log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--antennas" ; CommandLineBinding:shellQuote false ] ; sld:default "-1" ; sld:type xsd:string , sld:null . sld:default 5e-01 ; sld:type xsd:float , sld:null . sld:default "TGSS" ; sld:type xsd:string , sld:null . rdfs:comment "Provide state information for collecting antenna statistics" ; sld:default "NONE" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default false ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "count.savetojson=True" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type xsd:int , sld:null . rdfs:comment "Input Measurement Set string (including dummy.ms)" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "msin=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out.json" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "logs" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "BLsmooth.log" ] ; sld:type cwl:File . sld:default 16 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--timeslots" ; CommandLineBinding:shellQuote false ] ; sld:default "0,10,0" ; sld:type xsd:string , sld:null . cwl:source ; sld:default "12.21kHz" . cwl:source , ; cwl:valueFrom "$(self.join(''))" . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msout_name)" ] ; sld:type cwl:Directory . cwl:source . cwl:source . sld:default 8e-01 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-name" ; CommandLineBinding:shellQuote false ] ; sld:default "image" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-channels-out" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:int , sld:null . sld:default 8 ; sld:type xsd:int , sld:null . sld:default "40asec" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--wideband True" ; CommandLineBinding:shellQuote false ] ; sld:default true ; sld:type xsd:boolean , sld:null . rdfs:label "losoto_plot_P2" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . rdfs:comment "Radius of the skymodel" ; sld:default 5e+00 ; sld:type xsd:float , sld:null . sld:default -3.14e+00 , 3.14e+00 . rdfs:label "concat_logfiles_predict_targ" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Output Measurement Set" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ] ; sld:default "." ; sld:type xsd:string , sld:null . sld:default 9999999 , 150 . sld:default 16 ; sld:type xsd:int , sld:null . rdfs:comment "Add this step-name into the file-names of the output files." ; sld:default ".ms" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "" ; sld:type xsd:string , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:Directory . cwl:source . rdfs:label "prep_flags_join" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "verbose output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-v" ] ; sld:default true ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "plot_unflagged_fraction*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default false . 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 ] ; sld:type cwl:Directory . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-taper-gaussian" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , xsd:string , sld:null . cwl:source . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solsetName" ] ; sld:default "target" ; sld:type xsd:string , sld:null . rdfs:label "compare_station_list" ; cwl:in , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "uvplot*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 1e-30 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outh5parmname)-parm_collector_output*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "save_logfiles" ; cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.overwrite=True" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true ; sld:type xsd:boolean , sld:null . rdfs:comment "MS containing the target" ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "array_factor" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.sources=" ; CommandLineBinding:separate false ; cwl:valueFrom "[$(self.join(','))]" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . sld:default "Ateamclipper" . sld:default "Dysco" . sld:default "*&" ; sld:type xsd:string , sld:null . rdfs:comment "Column name to smooth" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-i" ] ; sld:default "DATA" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.storagemanager.databitrate=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:default "dpppconcat" . cwl:source . cwl:outputSource ; sld:type cwl:Directory . cwl:source ; sld:default 1 . cwl:linkMerge "merge_flattened" ; cwl:outputSource , , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 ] . cwl:source . sld:default true . sld:default "CS001HBA0" ; sld:type xsd:string , sld:null . 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 true ; sld:type xsd:boolean , sld:null . rdfs:comment "Specify proxy port if necessary" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--proxyport" ] ; sld:type xsd:int , 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 . sld:default "findRefAnt" . sld:default false ; sld:type xsd:boolean , sld:null . sld:default "TGSS" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "python3" "check_fraction.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import sys\nimport json\nimport shutil\nimport os\n\nfrom check_unflagged_fraction import main as check_unflagged_fraction\n\nms = sys.argv[1]\ninputs = json.loads(r\"\"\"$(inputs)\"\"\")\nmin_fraction = inputs['min_fraction']\n\noutput = check_unflagged_fraction(ms, min_fraction=min_fraction, print_fraction=True)\n\nfilename = os.path.basename(output['filename'].rstrip('/'))\nunflagged_fraction = output['unflagged_fraction']\nflagged = output['flagged']\n\ncwl_output = {}\ncwl_output['unflagged_fraction'] = unflagged_fraction\n\nif flagged != 'None':\n shutil.move(filename, filename.lstrip('out_'))\n cwl_output['filename'] = 'None'\nelse:\n cwl_output['filename'] = filename\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n" ; cwl:entryname "check_fraction.py" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "check_unflagged_fraction_err.log" ; cwl:stdout "check_unflagged_fraction.log" . sld:type xsd:int , sld:null . rdfs:comment "Antenna string to be processed" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--bad_antennas" ] ; sld:default "*&" ; sld:type xsd:string , sld:null . rdfs:comment "Number of time slots on which a solution is assumed to be constant (same as CellSize.Time in BBS).\n0 means all time slots. Note that for larger settings of solint, and specially for solint = 0,\nthe memory usage of gaincal will be large (all visibilities for a solint should fit in memory).\n" ; sld:default 1 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "summary*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Output JSON" ; cwl:outputBinding [ CommandOutputBinding:glob "*.json" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:type xsd:string . sld:default 5e-01 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logname)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logname)" ] ; sld:type cwl:File . rdfs:comment "Size of the markers in the 2D plot. By default 2.\n" ; sld:default 2 ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "concat" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , . cwl:outputBinding [ CommandOutputBinding:glob "add_missing_stations*.log" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "predict.usebeammodel=True" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "add_missing_stations" ; cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "" ; sld:type xsd:string , sld:null . rdfs:label "BLsmooth" ; cwl:in , , , ; cwl:out , ; cwl:run . rdfs:label "concat_logfiles_applygsm" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--limits" ; CommandLineBinding:shellQuote false ] ; sld:default ",,," ; sld:type xsd:string , sld:null . sld:default "[CR]S*&" ; sld:type xsd:string , sld:null . sld:default "ftp://ftp.aiub.unibe.ch/CODE/" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[applycal,count]" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; 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:linkMerge "merge_flattened" ; cwl:source . sld:default "time" . 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 "Specify column to flag" ; cwl:inputBinding [ CommandLineBinding:prefix "-column" ] ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.datacolumn=" ; CommandLineBinding:separate false ] ; sld:default "MODEL_DATA" ; sld:type xsd:string , sld:null . rdfs:comment "Gives an indication on how the smoothing varies with" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-s" ] ; sld:default 5e-01 ; sld:type xsd:float , sld:null . sld:default "make_sourcedb_target.log" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.writefullresflag=True" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "out.MS" ; sld:type xsd:string . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "H5parm to which this action should be performed." ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:default "output.h5" ; sld:type cwl:File . sld:default true ; sld:type xsd:boolean , sld:null . sld:default false . rdfs:label "dpppconcat" ; cwl:in , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . sld:default "prefactor" . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "\"uv coverage of the target pointing: $(self)\"" . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source ; sld:default false . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "avg.freqresolution=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "12.205kHz" ; sld:type xsd:string , sld:null . sld:default "check_unflagged_fraction" . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "gaincal.nchan=" ; CommandLineBinding:separate false ] ; sld:default 0 ; sld:type xsd:int , sld:null . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File , sld:null . a cwl:ExpressionTool ; rdfs:label "check_filtered_MS_array" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n if (inputs.input.length == 0) {\n throw new Error(\"No MS files meet the minimum unflagged fraction set by min_unflagged_fraction\")\n } else {\n return {'output': inputs.input}\n }\n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:label "gsmcal" ; cwl:in , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , ; cwl:run . a cwl:ExpressionTool ; rdfs:label "merge_array" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var out_dir = []\n for(var i=0; i ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:label "make_parset" ; cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . rdfs:label "concat_logfiles_clipper_targ" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "list of flagged antennas" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "steps=[filter,gaincal,count]" ) ; cwl:baseCommand ( "DP3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs , , , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "gaincal_err.log" ; cwl:stdout "gaincal.log" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:default "pol" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.storagemanager=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote false ] ; sld:default "" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "workdir/out_*" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "Ateamclipper.txt" ] ; sld:type cwl:File . 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: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: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: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: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 "$(inputs.flagged_fraction_dict)" ; cwl:entryname "input.json" ] ; cwl:listing [ cwl:entry "import sys\nimport json\nimport re\nimport ast\n\ninputs = json.loads(r\"\"\"$(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:InlineJavascriptRequirement ] ; cwl:stderr "findRefAnt_err.log" ; cwl:stdout "findRefAnt.log" . sld:default 10 ; sld:type xsd:int , sld:null . rdfs:comment "Output solution table (has to be different from input solution table)" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--soltab_out" ] ; sld:default "GSMphase" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . cwl:source . rdfs:label "concat_logfiles_RefAnt" ; cwl:in , ; cwl:out ; cwl:run . 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 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "filter.baseline=" ; CommandLineBinding:separate false ; CommandLineBinding:shellQuote true ; cwl:valueFrom "$(self)" ] ; sld:type xsd:string , sld:null . rdfs:comment "overwrite output" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-c" ] ; sld:default false ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . sld:default true ; sld:type xsd:boolean , sld:null . sld:default 10 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename1)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . rdfs:comment "IONEX Server path" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--server" ] ; sld:default "ftp://ftp.aiub.unibe.ch/CODE/" ; sld:type xsd:string , sld:null . sld:default true . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . sld:default 30 ; sld:type xsd:int , sld:null . rdfs:comment "Output solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insoltab" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" "import sys\nimport json\nfrom getTargetName import main as getTargetName\n\nmss = sys.argv[1:]\n\noutput = getTargetName(mss)\n\ntargetName = output['targetName']\ncwl_output = {\"targetName\": targetName}\n\nwith open('./out.json', 'w') as fp:\n json.dump(cwl_output, fp)\n \n" ) ; cwl:baseCommand ( "python3" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "lofareosc/prefactor3-cwl" ] ; cwl:inputs ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.msin)" ] ] ; cwl:stderr "get_targetname_err.log" ; cwl:stdout "get_targetname.log" . sld:default "48.82kHz" ; sld:type xsd:string , sld:null . sld:default "MODEL_DATA" . cwl:source ; sld:default true . sld:default "" . rdfs:label "final_flags_join" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . rdfs:label "write_solutions" ; cwl:in , , , , , , ; cwl:out , ; cwl:run . rdfs:comment "List of h5parm files" ; cwl:format ; cwl:inputBinding [ CommandLineBinding:position 0 ] ; sld:type cwl:File . cwl:source . sld:default "97.64kHz" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "DATA" . cwl:source . cwl:source . rdfs:comment "MS set output" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "count.jsonfilename=" ; CommandLineBinding:separate false ] ; sld:default "out.json" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jsonfilename)" ; CommandOutputBinding:outputEval "$(JSON.parse(self[0].contents).flagged_fraction_dict)" ; cwl:loadContents true ] ; sld:type xsd:string . sld:default "CasA" , "CygA" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default 4 ; sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(self+'_structure')" . sld:default 4 ; sld:type xsd:int , sld:null . sld:default "Dysco" . sld:default true ; sld:type xsd:boolean , sld:null . sld:default true . sld:default "DATA" . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "msout.writefullresflag=True" ; CommandLineBinding:shellQuote false ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--insolset" ] ; sld:default "sol000" ; sld:type xsd:string , sld:null . sld:default "ftp://ftp.aiub.unibe.ch/CODE/" ; sld:type xsd:string , sld:null . cwl:source . sld:default 10 ; sld:type xsd:int , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default 5 ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Output text" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outbasename+'_structure.txt')" ] ; sld:type cwl:File . rdfs:label "ms_concat" ; cwl:in , , ; cwl:out , , , ; cwl:run . rdfs:comment "Input solset name" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--solset" ] ; sld:default "target" ; sld:type xsd:string , sld:null . sld:default "phase" ; sld:type xsd:string , sld:null . sld:default 1e-03 . rdfs:comment "specifies a customized strategy\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-strategy" ; CommandLineBinding:separate true ; CommandLineBinding:shellQuote false ] ; sld:default "$PREFACTOR_DATA_ROOT/rfistrategies/lofar-default.lua" ; sld:type cwl:File , xsd:string , sld:null . 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:type [ sld:items cwl:Directory ; sld:type sld:array ] . 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 . a cwl:Workflow ; rdfs:label "finalize" ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . 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 ] . rdfs:label "make_sourcedb_ateam" ; cwl:in , ; cwl:out , ; cwl:run . rdfs:comment "Output Measurement Set" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.msin.basename)" ] ; sld:type cwl:Directory . sld:default "time" . rdfs:comment "Input measurement set" ; sld:type cwl:Directory . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "TGSS" ; sld:type xsd:string , sld:null . rdfs:comment "Output image" ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputimage)" ] ; sld:type cwl:File . sld:default "DATA" .