@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 ResourceRequirement: . cwl:source . cwl:default true . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:type cwl:File . cwl:default "alignments.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-alignments" ] ; sld:type xsd:string . rdfs:label "Resolve Annotation Conflicts" ; cwl:in , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:default "proteins.seq_ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-min_seq_len" ] ; sld:type xsd:int , sld:null . cwl:default "GeneMark_hmm_combined.mod" ; sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "gpx_qdump" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . cwl:default "workpath" ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-expansion-ratio" ] ; sld:type xsd:float . cwl:source . cwl:default "blastdb" ; sld:type xsd:string . cwl:source . cwl:default "output.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:default "from-stop-to-stop" ; cwl:inputBinding [ CommandLineBinding:prefix "-allowable-starts" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:default 120 . cwl:source . sld:type cwl:File . rdfs:label "Search All HMMs I" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:Directory . 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 . cwl:source . cwl:default "review.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-review" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-align-fmt" ] ; sld:type xsd:string . cwl:default 60 . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:default "accept.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-accept" ] ; sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:default 5000 . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:default "sequences.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:type xsd:string . cwl:default "output" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null . cwl:source , . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:default "prot.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-prot" ] ; sld:type xsd:string . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "gp_getorf" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_getorf" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "hmmsearch_wnode" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:default "entries.asnb" ; cwl:inputBinding [ CommandLineBinding:prefix "-seq-output" ] ; sld:type xsd:string , sld:null . cwl:default true . a cwl:CommandLineTool ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:inputs , , , , ; cwl:outputs , , . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:default "marked-annotation.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-marked-annotation" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Map HMM Hits" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bacterial_hit_mapping" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# aligns.mft created for bacterial_hit_mapping from input hmm_hits Array of Files\\n'; for (var i = 0; i < inputs.hmm_hits.length; i++) { blob += inputs.hmm_hits[i].path + '\\n'; } return blob; }" ; cwl:entryname "aligns.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preliminary_models_name)" ] ; sld:type cwl:File . cwl:default "preliminary-models.asn" . cwl:source . cwl:default true . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-no-compart" ] ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . rdfs:label "Run GeneMark Training (genemark_post)" ; cwl:in , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File , sld:null . sld:type cwl:Directory . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:source . cwl:default "models.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:default 180 . cwl:inputBinding [ CommandLineBinding:prefix "-seq_entries" ] ; sld:type cwl:File . rdfs:label "Get_off_frame_ORFs task node" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int , sld:null . cwl:default "seq-align" . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . sld:type cwl:Directory . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-aligns" ] ; sld:type cwl:File . cwl:in , , , , , , ; cwl:out ; cwl:run . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs . 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 "all-proteins.ids" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tmp)/$(inputs.out_hmm_params_name)" ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "workdir" . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-annot" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type cwl:File . cwl:source , , , , , . a cwl:CommandLineTool ; rdfs:label "Get off-frame ORFs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "get_off_frame_orfs" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . a cwl:Workflow ; rdfs:label "hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs . cwl:source . a cwl:CommandLineTool ; rdfs:label "bacterial_resolve_conflicts" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "bacterial_resolve_conflicts" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# features.mft created for bacterial_resolve_conflicts from input features Array of Files\\n'; if ( ! inputs.hasOwnProperty('features') ) { return blob; }; for (var i = 0; i < inputs.features.length; i++) { blob += inputs.features[i].path + '\\n'; } return blob; }" ; cwl:entryname "features.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# prot.mft created for bacterial_resolve_conflicts from input prots Array of Files\\n'; if ( ! inputs.hasOwnProperty('prots') ) { return blob; }; for (var i = 0; i < inputs.prots.length; i++) { blob += inputs.prots[i].path + '\\n'; } return blob; }" ; cwl:entryname "prot.mft" ] ] . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default "prot.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; sld:type xsd:string , sld:null . cwl:default "*" . cwl:default ".xml" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . sld:type cwl:File . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-selenocysteines" ; cwl:valueFrom "$(inputs.selenocysteines.path)/$(inputs.selenocysteines_db)" ] ; sld:type xsd:string . 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 ] . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.models_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . cwl:source . cwl:default "models_training.asn" . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.marked_annotation_name)" ] ; sld:type cwl:File . cwl:default "features.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-features" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default "hmm_hits.asn" . cwl:source , . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:default "mapped-hmm-hits.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File . cwl:source . sld:type cwl:Directory . sld:type cwl:Directory . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:default "jobs" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:default "aligns.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-aligns-manifest" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . sld:type cwl:Directory . cwl:default "proteins.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . 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:default "seq-entries-b" ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . 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:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-product-id-prefix" ] ; sld:type xsd:string , sld:null . cwl:default 200 . cwl:default 0e+00 . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:default "preliminary-models.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . 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:inputs , , , , ; cwl:outputs , , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.review_name)" ] ; sld:type cwl:File . cwl:default 42 ; cwl:inputBinding [ CommandLineBinding:prefix "-minsize" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "genemark_post" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "genemark_post" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-path" ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.accept_align_name)" ] ; sld:type cwl:File . cwl:default "accept-align.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-accept-align" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:type cwl:File . cwl:default "LDS2" ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "genemark_training" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "genemark" ) ; 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 [ cwl:entry "${ var blob = '# sequences.mft created for genemark_training from input sequences File\\n'; if ( inputs.sequences == null) { return blob; } else { return blob + inputs.sequences.path; } }" ; cwl:entryname "sequences.mft" ] ; cwl:listing [ cwl:entry "${ var blob = '# annotation.mft created for genemark_training from input annotation File\\n'; if ( inputs.annotation == null ) { return blob; } else { return blob + inputs.annotation.path; } }" ; cwl:entryname "annotation.mft" ] ; cwl:listing [ cwl:entry "${ var blob = '# alignments.mft created for genemark_training from input alignments File\\n'; if ( inputs.alignments == null ) { return blob; } else { return blob + inputs.alignments.path; } }" ; cwl:entryname "alignments.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . sld:type xsd:boolean . cwl:source . cwl:in , ; cwl:out , , ; cwl:run . cwl:outputSource ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:default "fam.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:default "annotation.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type xsd:string . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; sld:type cwl:Directory . cwl:default true . sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:default "." ; cwl:inputBinding [ CommandLineBinding:prefix "-tmp" ] ; sld:type xsd:string . rdfs:label "Run GeneMark Training, genemark" ; cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . cwl:default 10000 ; cwl:inputBinding [ CommandLineBinding:prefix "-max-seq-gap" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-pre-annot" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:type cwl:Directory , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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:inputs ; cwl:outputs ; cwl:stdout "cat.out" . cwl:default "all-proteins.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-out-product-ids" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; sld:type cwl:Directory . cwl:default "marked-annotation.asn" . cwl:source .