@prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns2: . @prefix SoftwarePackage: . @prefix ns1: . @prefix NetworkAccess: . @prefix SoftwareRequirement: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix ResourceRequirement: . @prefix ExpressionTool: . a cwl:Workflow ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "*summary.ko" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , ; cwl:cwlVersion ; 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--pfam-name" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ko" ] ; sld:type cwl:File , xsd:string . cwl:in , , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.format == 'tsv')" . sld:type cwl:File . sld:default "n" ; sld:type xsd:string , sld:null . a cwl:Workflow ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Tool does chunking of input table by number of lines in line_number. If initial file has less number of lines than line_number: output == input; Else if file was chunked: output == [ prefix_NUMBER.ext]; ( NUMBER has 2 digits format, ext == nameext of infile)" ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( "-d" "--numeric-suffixes=1" "-a" "3" ) ; cwl:baseCommand ( "split" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "debian:stable-slim" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 5000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:File , sld:null . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "InterProScan*.yaml" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*summary.ips" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--antismash-name" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . rdfs:label "Interpro scan results in TSV format" ; cwl:format ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "KO*.yaml" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix)*" ; CommandOutputBinding:outputEval "${\n if (self.length == 0) {\n return [inputs.infile]\n }\n if (self.length == 1) {\n self[0].basename = inputs.infile.basename\n return self\n }\n\n var list_new_files = [];\n for (var i = 0; i < self.length; ++i) {\n var cur_file = self[i];\n cur_file.basename = cur_file.basename + inputs.infile.nameext;\n list_new_files.push(cur_file);\n }\n return list_new_files\n}\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "pfam*.yaml" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File , xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*summary.pfam" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-h" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( "-p" "8" "-c" ) ; cwl:baseCommand ( "pigz" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.bash-scripts:v1.3" ] ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 200 ] ; cwl:stdout "$(inputs.uncompressed_file.basename).gz" . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.uncompressed_file.basename).gz" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.nameroot.split('_CDS')[0]).summary.ko" . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:linkMerge "merge_nested" ; cwl:pickValue "all_non_null" ; cwl:source , , . cwl:source . sld:type cwl:File . cwl:source . cwl:linkMerge "merge_nested" ; cwl:pickValue "all_non_null" ; cwl:source , , . cwl:source ; cwl:valueFrom "$(self.nameroot.split('_CDS')[0]).summary.antismash" . cwl:source . sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "functional-annotation" ] ; sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.nameroot).pfam" . cwl:outputBinding [ CommandOutputBinding:glob "stderr.txt" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gather summary file from InterProScan" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:baseCommand ( "write_summaries.py" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.python3:v3.1" ] ; cwl:inputs , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9500 ] . cwl:source ; cwl:valueFrom "$(self.nameroot.split('_CDS')[0]).summary.ips" . sld:type xsd:string . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:outputSource , ; cwl:pickValue "all_non_null" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type sld:null ; sld:type [ sld:items cwl:File , sld:null ; sld:type sld:array ] . cwl:source . a cwl:ExpressionTool ; ns2:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var newArray= [];\n for (var i = 0; i < inputs.arrayTwoDim.length; i++) {\n for (var k = 0; k < inputs.arrayTwoDim[i].length; k++) {\n newArray.push((inputs.arrayTwoDim[i])[k]);\n }\n }\n return { 'array1d' : newArray }\n}" ; cwl:cwlVersion ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:int , sld:null . cwl:inputBinding [ cwl:loadContents true ] ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "generate all functional stats and orf stats" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder "EMBL - European Bioinformatics Institute" ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:baseCommand ( "functional_stats.py" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.python3:v3.1" ] ; 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:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 8000 ] . cwl:outputBinding [ CommandOutputBinding:glob "stdout.txt" ] ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "--input-file" ] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out , , , ; cwl:run . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.input_table.nameroot)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run ; cwl:when "$(inputs.format == 'fasta')" . sld:type xsd:int , sld:null . sld:type xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self.nameroot).summary.go" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.infile.basename).chunks" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*summary.antismash" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . cwl:in , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type cwl:Directory . sld:type cwl:File , xsd:string . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--config" ] ; sld:default "go_summary-config.json" ; sld:type cwl:File , xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "-a" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:Directory . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--ips-name" ] ; sld:type xsd:string . cwl:format ; cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:baseCommand ( "add_header" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.bash-scripts:v1.3" ] ; cwl:hints [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 200 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.input_table.nameroot)" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:pickValue "all_non_null" ; cwl:source , . sld:type xsd:string . cwl:source . sld:default 10000000 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--ko-name" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-a" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( "--output-file" "$(inputs.output_name)" ) ; cwl:baseCommand ( "go_summary_pipeline-1.0.py" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:SoftwareRequirement ; SoftwareRequirement:packages [ SoftwarePackage:package "owltools" ; SoftwarePackage:specs ; SoftwarePackage:version "8d53bbce1ffe60d9aa3357c1001599f9a882317a" ] ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.go-summary:v1.0" ] ; 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:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:stderr "stderr.txt" ; cwl:stdout "stdout.txt" . a cwl:Workflow ; ns2:original_cwlVersion "v1.2.0-dev2" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "*.go_slim" ] ; sld:type cwl:File . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "*.fasta*" ; CommandOutputBinding:outputEval "${\n if (self.length == 1) {\n self[0].basename = inputs.infile.basename\n return self\n }\n else {\n var list_new_files = [];\n for (var i = 0; i < self.length; ++i) {\n var cur_file = self[i];\n cur_file.basename = inputs.infile.nameroot + \"_\" + cur_file.basename.split('.').pop() + inputs.infile.nameext;\n list_new_files.push(cur_file);\n }\n return list_new_files }\n}\n" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "tsv" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . a cwl:CommandLineTool ; rdfs:label "Parse Pfam hits from Interpro annotation output" ; ns2:original_cwlVersion "v1.0" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( "awk" "/Pfam/" "$(inputs.interpro)" ) ; cwl:baseCommand () ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "debian:stable-slim" ] ; 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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMax 1 ; ResourceRequirement:ramMin 200 ] ; cwl:stdout "$(inputs.outputname)" . cwl:source . cwl:source ; cwl:valueFrom "$(self.nameroot.split('_CDS')[0]).summary.pfam" . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-c" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Tool creates file NAME.chunks and add inside basenames of given list of files" ; ns2:original_cwlVersion "v1.2" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n var return_string = \"\";\n for (var i = 0; i < inputs.list_chunks.length; ++i) {\n var cur_file = inputs.list_chunks[i];\n return_string = return_string + cur_file.basename + \"\\n\";\n }\n return return_string;\n}\n" ] ) ; cwl:baseCommand ( "echo" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "debian:stable-slim" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 500 ] ; cwl:stdout "$(inputs.infile.basename).chunks" . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Tool does chunking of input fasta by target size using genometools. If initial file has less number of lines than line_number: output == input; Else if file was chunked: output == [ prefix_NUMBER.ext]; ( NUMBER has 2 digits format, ext == nameext of infile)" ; ns2:original_cwlVersion "v1.1" ; ns1:copyrightHolder [] ; ns1:license "https://www.apache.org/licenses/LICENSE-2.0" ; cwl:arguments ( [ CommandLineBinding:prefix "-n" ; cwl:valueFrom "${\n if (inputs.size_limit) { return inputs.size_limit }\n if (inputs.type_fasta == 'n') {\n return 1980\n }\n if (inputs.type_fasta == 'p') {\n return 1442\n }\n}\n" ] ) ; cwl:baseCommand ( "split_fasta_by_size.sh" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "microbiomeinformatics/pipeline-v5.split-fasta:v2" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 5000 ] . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "*.go" ] ; sld:type cwl:File . sld:default "n" ; sld:type xsd:string , sld:null . cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "antismash*.yaml" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source ; cwl:valueFrom "$(self.nameroot)_" . rdfs:label "Pfam results only" ; cwl:format ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outputname)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-l" ] ; sld:type xsd:int .