@prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix ScatterMethod: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "plot-figs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/bin/combine_results.R" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/figures" ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "correlation" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sampleType" ] ; sld:default "all" ; sld:type xsd:string , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.tsv" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "prot-deconv" ; ns1:original_cwlVersion "v1.1" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-epic-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-epic-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "corrXcelltypes.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature\n var name = inputs.sampleType + '-' + inputs.cancerType + '-' + inputs.mrnaAlg + '-to-' + inputs.protAlg +'-'+ mat + '-cellTypecorr.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-cibersort-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-cibersort-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "file.tsv" ; CommandOutputBinding:outputEval "${\n var name = inputs.cancerType + '-' + inputs.sampleType + '-' + 'mrna-raw.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "corr.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature\n var name = inputs.sampleType + '-' + inputs.cancerType + '-' + inputs.mrnaAlg + '-to-' + inputs.protAlg +'-'+ mat + '-corr.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.alg.trim() == \"bayesdebulk\")" . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "get-signature-matrix" ; ns1:original_cwlVersion "v1.1" ; cwl:arguments ( "/getSigMatrices.R" ) ; cwl:arguments ( "/getSigMatrices.R" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/signature_matrices" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/signature_matrices" ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "mrna-data-cwl-tool" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/mRNADataSetsCLI.py" ) ; cwl:baseCommand ( "python" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/mrna-data" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-bayesdebulk-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-bayesdebulk-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.alg.trim() == \"epic\")" . cwl:inputBinding [ CommandLineBinding:prefix "--transcriptomics" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "*.pdf" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "*.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.txt" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:string . cwl:source . a cwl:Workflow ; rdfs:label "mrna-deconv" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.alg.trim() == \"cibersort\")" . sld:type xsd:string . cwl:source . cwl:in , , , , , , ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "scatter-test" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "deconv-corrXcelltypes-cwl-tool" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/correlationXcelltypes.py" ) ; cwl:baseCommand ( "python" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/correlation" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "prot-data-cwl-tool" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/protDataSetsCLI.py" ) ; cwl:baseCommand ( "python" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/prot-data" ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--signatureMatrix" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--signatureMatrix" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--rowMeansImputation" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--rowMeansImputation" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--sampleType" ] ; sld:default "all" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "run-cibersort-tool" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--vanilla" "/bin/cibersort.r" ) ; cwl:arguments ( "--vanilla" "/bin/cibersort.r" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/cibersort:latest" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/cibersort:latest" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-mcpcounter-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-mcpcounter-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--spearOrPears" ] ; sld:default "spearman" ; sld:type xsd:string . cwl:source . sld:type xsd:string . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.alg.trim() == \"mcpcounter\")" . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:in , , , , ; cwl:out , , , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:flat_crossproduct . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--transcriptomics" ] ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--cancerType" ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:valueFrom "cellType" . a cwl:CommandLineTool ; rdfs:label "run-epic-tool" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--vanilla" "/bin/epic.r" ) ; cwl:arguments ( "--vanilla" "/bin/epic.r" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/epic" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/epic" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "--proteomics" ] ; sld:type cwl:File . sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "file.tsv" ; CommandOutputBinding:outputEval "${\n var name = inputs.cancerType + '-' + inputs.sampleType + '-' + 'prot-raw.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-xcell-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "deconvoluted.tsv" ; CommandOutputBinding:outputEval "${\n var mat = inputs.signature.nameroot\n var cancer = inputs.expression.nameroot\n var name = cancer + '-xcell-'+ mat + '.tsv'\n self[0].basename = name;\n return self[0]\n }\n" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "run-deconv" ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "rep-bulk" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "/bin/main_docker.R" ) ; cwl:arguments ( "/bin/main_docker.R" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/in-progress" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/in-progress" ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--expressionFile" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--expressionFile" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "call-deconv-and-cor" ; 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:InlineJavascriptRequirement ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--cancerType" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--proteomics" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "run-mcpcounter-tool" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--vanilla" "/bin/mcpcounter.r" ) ; cwl:arguments ( "--vanilla" "/bin/mcpcounter.r" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/mcpcounter" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/mcpcounter" ] . a cwl:CommandLineTool ; rdfs:label "deconv-corr-cwl-tool" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/correlation.py" ) ; cwl:baseCommand ( "python" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/correlation" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "run-xcell-tool" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--vanilla" "/bin/xcell.r" ) ; cwl:arguments ( "--vanilla" "/bin/xcell.r" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:baseCommand ( "Rscript" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/xcell" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "tumordeconv/xcell" ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--spearOrPears" ] ; sld:default "spearman" ; sld:type xsd:string . cwl:outputSource , , , , ; cwl:pickValue "first_non_null" ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.alg.trim() == \"xcell\")" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File .