@prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Dirent: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix rdfs: . @prefix ResourceRequirement: . @prefix CommandOutputBinding: . @prefix ns1: . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_orthologs)" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in , , , , , , , , ; cwl:out ; cwl:run [ a cwl:CommandLineTool ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.molecules)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.molecules)" ] ] ] . sld:type xsd:boolean . a cwl:Workflow ; rdfs:label "cluster_blastp_wnode and gpx_qdump combined" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . sld:type xsd:int . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-s_coverage_threshold" ] ; sld:default 9e-01 ; sld:type xsd:float , sld:null . cwl:source . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "Propagate symbols to genes" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . rdfs:label "Get Assemblies for Orthologs GenColl ASN" ; cwl:in , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . sld:default false . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o_stats" ] ; sld:default "stats.xml" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o_orthologs" ] ; sld:default "orthologs.rpt" ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-short-protein-threshold" ] ; sld:type xsd:int , sld:null . sld:default "6000000000" . rdfs:label "Extract Orthologous Prokaryotic Proteins" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-orthologs" ] ; sld:type cwl:File . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:default ".xml" ; sld:type xsd:string , sld:null . sld:default 1 . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "gc_get_assembly" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gc_get_assembly" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-offset" ] ; sld:type xsd:long , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-files-per-dir" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default 1e-03 . a cwl:Workflow ; rdfs:label "protein_extract" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "gencoll.asn" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:string . cwl:source . sld:type xsd:int . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-release_id_list" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; sld:default "ids.mft" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; sld:type xsd:float , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "gpx_qdump" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . sld:type xsd:string . sld:type xsd:string . sld:default "blastdir" . cwl:source . a cwl:CommandLineTool ; rdfs:label "find_orthologs" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "find_orthologs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# annots1.mft created for find_orthologs from input annots1 File\\n'; if(inputs.annots1 != null) { blob += inputs.annots1.path + '\\n'; } return blob; }" ; cwl:entryname "annots1.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "out_asn_name.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-hits-output" ] ; sld:default "retrieved_hits.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:default "jobs" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "propagated_gene_symbols_annot.asn" ; sld:type xsd:string , sld:null . sld:type cwl:File . sld:type xsd:int . sld:type cwl:File . sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-check_exome" ] ; sld:default true ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:string . cwl:source . sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.not_found_output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; sld:type xsd:int , sld:null . sld:type xsd:string , sld:null . sld:type cwl:File . sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:comment "This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n proteins:\n default:\n class: File\n path: '/dev/null'\n basename: 'null'\n contents: ''\n" ; rdfs:label "gpx_qsubmit" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ cwl:entry "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ; cwl:entryname "ids.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . sld:type cwl:File . sld:default 250 . sld:default true . sld:type cwl:File . sld:default 0 . sld:default "predicted-protein" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; sld:type cwl:File . rdfs:label "BLASTp Current Prokaryotic Proteins vs Orthologs/cat aligns" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; sld:type xsd:float , sld:null . sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_asn_name)" ] ; sld:type cwl:File . rdfs:label "Find Prokaryotic Orthologs" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "gp_fetch_sequences" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_fetch_sequences" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-annots1" ] ; sld:default "annots1.mft" ; sld:type xsd:string . cwl:source . cwl:source . sld:type xsd:float , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; sld:type xsd:string . cwl:source . cwl:outputSource , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "blastp_wnode_naming" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-blast-hits-sqlite-cache" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "Extract Orthologous Prokaryotic Proteins: fetch nucleotide ASN.1" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:default "input_text.asn" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:Directory . sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "output.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:in ; cwl:out ; cwl:run [ a cwl:CommandLineTool ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; 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: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)" ] ] ] . sld:type cwl:Directory . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . sld:default "orhologous.nucleotide.asn" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-not-found-output" ] ; sld:default "not_found.ids" ; sld:type xsd:string , sld:null . sld:type xsd:boolean . cwl:source . cwl:source . sld:type cwl:Directory , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-prot_similarity_threshold" ] ; sld:default 8e-01 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; sld:default "blastdb" ; sld:type xsd:string . rdfs:label "Prepare Annotation Input" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:default "subject" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . rdfs:label "BLASTp Current Prokaryotic Proteins vs Orthologs" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-q_coverage_threshold" ] ; sld:default 9e-01 ; sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "gcaccess_from_list" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . sld:default "prot" . sld:default "F" . cwl:inputBinding [ CommandLineBinding:prefix "-len" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "gc_get_molecules" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gc_get_molecules" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-max-objects" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "bacterial_orthology" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . a cwl:CommandLineTool ; rdfs:label "cwl split wrapper" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "split" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-gc2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:default 21 . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "proteins.asn" ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; sld:default "subject" ; sld:type xsd:string , sld:null . cwl:source . rdfs:label "Get Assemblies for Orthologs GenColl ASN/nucleotide ids" ; cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:label "Create Orthologous Prokaryotic Protein BLASTdb" ; cwl:in , , , ; cwl:out ; cwl:run . sld:default "concatenated.file" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-genus-list" ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default "no" . cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "asn_translated.asn" ; sld:type xsd:string , sld:null . sld:type xsd:int . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out , , ; cwl:run [ a cwl:CommandLineTool ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:inputs , , , , , ; cwl:outputs , , ] . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; sld:default "blastdb.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; sld:default "all" ; sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . sld:default 10000 . cwl:inputBinding [ CommandLineBinding:prefix "-level" ] ; sld:default "top-level" ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "update file set file_name=replace(file_name, rtrim(file_name, replace(file_name, '/', '')), '');" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "assembly.molecules.ids" ; sld:type xsd:string , sld:null . sld:default "*" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File , sld:null . sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "propagate_symbols_to_genes" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "propagate_symbols_to_genes" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default "blastp.align.asn" . cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; sld:default "LDS2" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-prot_hits" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "orf_hits_cache_retrieve" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "orf_hits_cache_retrieve" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${\n var blob = '# ids.mft created for orf_hits_cache_retrieve from input \"orfs\" Array of Files' +\n String.fromCharCode(10) ; \n for (var i = 0; i < inputs.orfs.length; i++) { \n blob += inputs.orfs[i].path + String.fromCharCode(10); \n } \n return blob; \n}" ; cwl:entryname "ids.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:File , sld:null . sld:default "asn-binary" . cwl:inputBinding [ CommandLineBinding:prefix "-class" ] ; sld:type xsd:string , sld:null . cwl:source . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; sld:default "found_ids.mft" ; sld:type xsd:string . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; sld:default "proteins.seq_ids" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . sld:default 1e+00 . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; sld:type xsd:string . sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; sld:default "found_ids.txt" ; sld:type xsd:string . cwl:source . sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:type xsd:string , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-orfs-manifest" ] ; sld:default "ids.mft" ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-blast-type" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . a cwl:Workflow ; rdfs:label "gp_makeblastdb" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-min-chunk-size" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; sld:type xsd:int , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-gc-cache" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . sld:default 6 . cwl:source . sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . sld:default true . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-items-per-chunk" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:type xsd:int . sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-max-chunk-size" ] ; sld:type xsd:long , sld:null . sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int , sld:null . sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . sld:default true . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; sld:type cwl:File , sld:null . sld:type xsd:boolean . cwl:source . a cwl:CommandLineTool ; rdfs:label "asn_translator" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asn_translator" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , . sld:default "AllSequences" . sld:type xsd:int . rdfs:label "Extract Protein Targets for Orthology" ; cwl:in , ; cwl:out , , ; cwl:run . cwl:source . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:source . sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "file concatenation" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:stdout "cat.out" . cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:int . sld:type xsd:boolean . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-gc1" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.hits_output_name)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:in , ; cwl:out ; cwl:run [ a cwl:CommandLineTool ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ] . cwl:source . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "concatenates input File[] to output File" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs ; cwl:stdout "$(inputs.output_file_name)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string . cwl:source . sld:type xsd:int , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "protein database for orhology graph" . cwl:source . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "jobs.xml" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "cluster_blastp_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cluster_blastp_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.lds2)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 5000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source .