@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix Dirent: . @prefix cwl: . @prefix ExpressionTool: . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${ var gc = inputs.gencode; var gc2 = \"\"; if( gc == 4 ) { gc2=\"othmito\"; } else if ( gc==6 ) { gc2=\"cilnuc\"; } else if ( gc == 9) { gc2 = \"echdmito\" } else if ( gc == 5) { gc2 = \"invmito\" } else if ( gc == 2) { gc2 = \"vertmito\" } else if ( gc == 3) { gc2 = \"ystmito\" } ; if ( gc2 != \"\" ) { return { \"output\": \"/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/tRNAscan-SE/production/lib/tRNAscan-SE/gcode/gcode.\"+gc2 }; } else { return { \"output\": null }; } }\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:default true . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${ return { \"value\": parseInt(inputs.input.contents) }; }\n" ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:int . cwl:default ".xml" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type xsd:int . cwl:source . cwl:source . cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "-A" ; cwl:valueFrom "${if (inputs.superkingdom==2157) { return true; } else {return false; } }" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "file concatenation" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "cat.out" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:type cwl:Directory . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, execution" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-X" "20" "-Q" "-H" "-b" "-q" "-nogenbank" ) ; cwl:baseCommand ( "trnascan_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . sld:type xsd:int . cwl:source . cwl:source . sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oasn)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . cwl:default true . sld:type xsd:int . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:default "gencode.txt" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string . cwl:in ; cwl:out , ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:default "struct.tar.gz" ; cwl:inputBinding [ CommandLineBinding:prefix "-ostruc" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ostruct)" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, transform" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-X" "20" ) ; cwl:baseCommand ( "trnascan_dump" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , . cwl:in , ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-superkingdom" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-superkingdom" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:default "intermediate.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "-B" ; cwl:valueFrom "${if (inputs.superkingdom==2) { return true; } else {return false; } }" ] ; sld:type xsd:boolean . cwl:source . a cwl:CommandLineTool ; rdfs:label "compute_gencode" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "compute_gencode" ) ; cwl:baseCommand ( "compute_gencode" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, scatter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:source . cwl:default "trnascan.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-oasn" ] ; sld:type xsd:string , sld:null . cwl:source . a cwl:Workflow ; rdfs:label "Run tRNAScan" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-gencode" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-gencode" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, gather" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-unzip" "*" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "cwl split wrapper" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "split" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs . sld:type cwl:File . cwl:source . cwl:source . cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ThirdParty/tRNAscan-SE/production/bin/tRNAscan-SE" ; cwl:inputBinding [ CommandLineBinding:prefix "-tRNAscan" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:default "jobs" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "trnascan_wnode and gpx_qdump combined" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string , sld:null . cwl:default "output" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null .