@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix Dirent: . @prefix cwl: . sld:type xsd:string , sld:null . cwl:source . cwl:source , . cwl:default "*" . sld:type cwl:File . cwl:source . sld:type cwl:Directory . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "protein_extract" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:inputs , , , , ; cwl:outputs , , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-wp-hashes" ] ; sld:type cwl:File . cwl:default "preliminary-models.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:default "models.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:type xsd:string . cwl:default "best_aligns.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; sld:type xsd:int , sld:null . rdfs:label "Name by WPs" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "application.log" ] ; sld:type cwl:File . cwl:default "annotation.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type xsd:string . cwl:default true . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:default "hmm-assignments.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:Directory . sld:type cwl:File , sld:null . cwl:default 113 . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.models_name)" ] ; sld:type cwl:File . cwl:default 5000 . cwl:default "output.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:inputs , , , , ; cwl:outputs , , . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:type cwl:Directory . cwl:source . sld:type cwl:Directory . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:default 180 . a cwl:CommandLineTool ; rdfs:label "identify_wp" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "identify_wp" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , ; cwl:outputs , , ; cwl:stderr "application.log" ; cwl:stdout "application.out" . cwl:outputBinding [ CommandOutputBinding:glob "application.out" ] ; sld:type cwl:File . rdfs:label "Run GeneMark" ; cwl:in , , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:source . cwl:default "hmm_hits.asn" . sld:type xsd:string . cwl:default "proteins.seq_ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.names)" ] ; sld:type cwl:File . cwl:default "jobs" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . rdfs:label "Resolve Annotation Conflicts/annotation" ; sld:type cwl:File . cwl:default "alignments.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-alignments" ] ; sld:type xsd:string . cwl:source . sld:type cwl:File . sld:type cwl:Directory . sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:default "all-proteins.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-out-product-ids" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-start-stop-allowance" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_align_name)" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "genemark" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "genemark" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${ if ( inputs.annotation == null ) { return ''; } else { return inputs.annotation.path; } }" ; cwl:entryname "annotation.mft" ] ; cwl:listing [ cwl:entry "${ if ( inputs.sequences == null) { return ''; } else { return inputs.sequences.path; } }" ; cwl:entryname "sequences.mft" ] ; cwl:listing [ cwl:entry "${ if ( inputs.alignments == null ) { return ''; } else { return inputs.alignments.path; } }" ; cwl:entryname "alignments.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . rdfs:label "goes to protein_alignment/Seed Search Compartments/compartments" ; cwl:outputSource ; sld:type cwl:File . cwl:default "blastdb" ; sld:type xsd:string . sld:type cwl:File , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gpx_qdump" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:inputs , , ; cwl:outputs . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type cwl:File . cwl:default true . cwl:default 120 . cwl:source . sld:type cwl:Directory . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-fast" ] ; sld:type xsd:boolean . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "assign_hmm" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "assign_hmm" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-path" ] ; sld:type cwl:Directory . cwl:source . cwl:default "annotation.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type xsd:string . rdfs:label "Map HMM Hits/align" ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; sld:type cwl:File . cwl:default "sequences.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:type xsd:string . cwl:in , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . sld:type cwl:Directory . rdfs:label "Search Naming HMMs" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:default "seq-entries" . cwl:outputSource ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:default true . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:default "fam.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; sld:type xsd:string , sld:null . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preliminary_models_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "genemark_post" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "genemark_post" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs . cwl:outputSource ; sld:type cwl:File . cwl:default "marked-annotation.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-marked-annotation" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:label "Run GeneMark (genemark_post)" ; cwl:in , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . a cwl:Workflow ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:type cwl:File . cwl:default 200 . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:default ".xml" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type xsd:boolean . cwl:source . sld:type cwl:Directory . sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:default "LDS2" ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:default "workpath" ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type cwl:Directory . cwl:source . cwl:default "marked-annotation.asn" . sld:type cwl:File . cwl:default "align.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oname)" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:default "best_aligns.asn" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:default "models.asn" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string , sld:null . cwl:default "update file set file_name=replace(file_name, rtrim(file_name, replace(file_name, '/', '')), '');" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string , sld:null . cwl:default true . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "cwl split wrapper" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "split" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . cwl:default "output" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:default "proteins.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "hmmsearch_wnode" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-backlog" "1" "-cut_ga" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; 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:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${ if ( inputs.hmms_tab == null ) { return ''; } else { return inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-params" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-min_seq_len" ] ; sld:type xsd:int , sld:null . rdfs:label "Filter Protein Alignments I/align" ; sld:type cwl:File . cwl:default 60 . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:label "Find Best Evidence Alignments" ; cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-pre-annot" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "hmmsearch_create_jobs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.marked_annotation_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)" ; 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:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "file concatenation" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "cat.out" . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "-tmp" ] ; sld:type xsd:string . cwl:source . cwl:default "preliminary-models.asn" . cwl:default "all-proteins.ids" . cwl:inputBinding [ CommandLineBinding:prefix "-selenocysteines" ; cwl:valueFrom "$(inputs.selenocysteines.path)/$(inputs.selenocysteines_db)" ] ; sld:type xsd:string . cwl:default 60 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "bact_best_evidence_alignments" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bact_best_evidence_alignments" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ncbi/gpdev:latest" ] ; 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:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = ''; for (var i = 0; i < inputs.align.length; i++) { blob += inputs.align[i].path + '\\n'; } return blob; }" ; cwl:entryname "align.mft" ] ; cwl:listing [ cwl:entry "$(inputs.annotation.path)" ; cwl:entryname "annotation.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; sld:type cwl:Directory . cwl:source , . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:default "names.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-onames" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; sld:type cwl:File . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . a cwl:CommandLineTool ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.in_lds2)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.in_lds2)" ] ] . cwl:source . cwl:default "workdir" . cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-annot" ] ; sld:type cwl:File . cwl:default true . rdfs:label "Extract Model Proteins" ; cwl:in , ; cwl:out , , ; cwl:run . rdfs:label "Assign Naming HMM to Proteins" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File .