@prefix LoadListingRequirement: . @prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Dirent: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . sld:type xsd:int . cwl:default "score>0 && pct_identity_gapopen_only > 35" . cwl:default "proteins.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-hits" ] ; sld:type cwl:File . cwl:default "blastdb" . cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "assign_cluster" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "assign_cluster" ) ; 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 "$(inputs.namedb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "blastp_wnode_naming" ; 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:ScatterFeatureRequirement ] . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "file concatenation" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "cat.out" . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-x" ] ; sld:type xsd:int . cwl:source . cwl:default "prot.seq_ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . sld:type xsd:int . cwl:source . cwl:default "annotation.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; sld:type xsd:int , sld:null . rdfs:label "Assign Clusters to Proteins" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; sld:type xsd:int , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "bact_annot_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bact_annot_filter" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = ''; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "annotation.mft" ] ] . sld:type xsd:boolean . cwl:default "no" . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:default "jobs" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . sld:type xsd:int . cwl:default 1 . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:default "13G" . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-margin" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:default 5e-01 . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-n" ] ; sld:type xsd:int , sld:null . sld:type xsd:boolean . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "align_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "align_filter" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . 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:prefix "-word_size" ] ; sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default "align.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:default 50 . sld:type cwl:Directory . cwl:source . cwl:source . cwl:default "no" . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "cluster_blastp_wnode" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "cluster_blastp_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 "${ 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 "${ var cs=0; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 false ; cwl:entry "${ var cs=1; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.lds2)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-group" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:default 1 . cwl:inputBinding [ CommandLineBinding:prefix "-defline-cleanup-rules" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; 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 ] . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string . cwl:default "align.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-d" ] ; sld:type cwl:Directory . cwl:default "precedences.tsv" ; cwl:inputBinding [ CommandLineBinding:prefix "-precedences" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:default "6000000000" . cwl:source . cwl:default true . cwl:source . cwl:default "proteins.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-proteins" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . cwl:default true . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . sld:type cwl:File . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:in , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:default "subject_coverage >= 10" . cwl:default 1e-01 . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type cwl:Directory . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 500 . cwl:default "ids.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . cwl:source . cwl:default false . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string , sld:null . cwl:default 120 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.xml_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int , sld:null . cwl:default 0 . cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; sld:type xsd:int , sld:null . cwl:default 10 . 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:inputs , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-hfmt" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-namedb" ; cwl:valueFrom "$(inputs.namedb_dir.path)/$(inputs.namedb)" ] ; sld:type xsd:string , sld:null . sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 . sld:type cwl:Directory . cwl:source . cwl:default 1 . sld:type cwl:File . cwl:default "F" . sld:type xsd:boolean . cwl:default "align-nomatch.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-onon-match" ] ; sld:type xsd:string . cwl:default true . cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.xml_jobs)" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . a cwl:Workflow ; rdfs:label "cluster_blastp_wnode and gpx_qdump combined" ; 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 ] . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type xsd:float , sld:null . cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:default "cdd" ; cwl:inputBinding [ CommandLineBinding:prefix "-b" ; cwl:valueFrom "$(inputs.b.path)/$(inputs.blastdb)" ] ; sld:type xsd:string . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:default 21 . a cwl:CommandLineTool ; rdfs:label "align_sort" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "align_sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-subject-whitelist" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:default true . cwl:source . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gp_fetch_sequences" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gp_fetch_sequences" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-cutoff" ] ; sld:type xsd:float , sld:null . sld:type xsd:string . cwl:default "other_assignments.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-other-assignments" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . cwl:default true . sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "prepare_sparclbl_input" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "prepare_sparclbl_input" ) ; 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 "${var blob = ''; for (var i = 0; i < inputs.other_assignments.length; i++) { blob += inputs.other_assignments[i].path + '\\n'; } return blob; }" ; cwl:entryname "other_assignments.mft" ] ] . cwl:default 21 . a cwl:CommandLineTool ; rdfs:label "sparclbl" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "sparclbl.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , ; cwl:outputs . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; sld:type cwl:File , 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:default 1.5e-01 . sld:type xsd:int . cwl:linkMerge "merge_flattened" ; cwl:source , , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ; sld:type xsd:int , sld:null . sld:type xsd:boolean . cwl:default "proteins.fa" . sld:type xsd:string . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.onon_match_name)" ] ; sld:type cwl:File . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; sld:type xsd:boolean , sld:null . cwl:default "blast_rules_db" , "blastdb" . cwl:source . sld:type cwl:File . cwl:default "F" . cwl:default "output.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:type xsd:boolean . cwl:source . sld:type cwl:Directory . cwl:source . cwl:default 1000000 . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type cwl:File . cwl:default "query,subject,-score,-num_ident,query_align_len,subject_align_len,query_start,subject_start" . cwl:source . sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; sld:type xsd:int , sld:null . rdfs:label "Find best protein hits" ; cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:int . cwl:default "protein_assignments.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ var blob = ''; for (var i = 0; i < inputs.blastdb_dir.length; i++) { blob += inputs.blastdb_dir[i].path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb_dir.length-1) blob += ','; } return blob; }" ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:default 5000 . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source , , , . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:default 60 . cwl:source . cwl:default "binary" . cwl:default ".xml" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . rdfs:label "Bacterial Annot Filter" ; cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . sld:type xsd:int . cwl:source . cwl:default 10000 . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . rdfs:label "Add Names to Proteins" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-long-model-limit" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . cwl:default true . sld:type xsd:int . cwl:source , . rdfs:label "Find Naming Protein Hits" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:default "subject" . cwl:inputBinding [ CommandLineBinding:prefix "-top" ] ; sld:type xsd:int , sld:null . cwl:default 5e-02 . cwl:default "subject" ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; sld:type xsd:string , sld:null . cwl:default true . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string . sld:type cwl:File , sld:null . cwl:default 20 . sld:type xsd:boolean . cwl:source . 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 "v1.0" ; cwl:baseCommand ( "gpx_qsubmit" ) ; 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 "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=0; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }" ] ; cwl:listing [ cwl:entry "${var blob = '';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ; cwl:entryname "ids.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "${ var cs=1; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:default "asn-binary" . cwl:default true . cwl:default true . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . rdfs:label "Assign Clusters to Proteins" ; cwl:in , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:default 6 . cwl:source . cwl:default "annotation.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "add_prot_names_to_annot" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "add_prot_names_to_annot" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = ''; for (var i = 0; i < inputs.proteins.length; i++) { blob += inputs.proteins[i].path + '\\n'; } return blob; }" ; cwl:entryname "proteins.mft" ] ] . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.precedence_filename)" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.protein_assignments_name)" ] ; sld:type cwl:File . cwl:default "seq-align" . cwl:source . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "asn2fasta" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "asn2fasta" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:default true . cwl:default "*" . cwl:inputBinding [ CommandLineBinding:prefix "-task" ] ; sld:type xsd:string , sld:null . cwl:default "blastp" . cwl:default 6 . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; sld:type xsd:string . sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:int , sld:null . cwl:default "output" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 180 . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-sure-cutoff" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_proteins_name)" ] ; sld:type cwl:File . rdfs:label "Prepare SPARCLBL input" ; cwl:in , , ; cwl:out , ; cwl:run . cwl:default "seq-align-set" . cwl:inputBinding [ CommandLineBinding:prefix "-submission-mode-genbank" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type cwl:File . cwl:default "out-annotation.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_name)" ] ; sld:type cwl:File . cwl:default "output_proteins.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:int , sld:null . cwl:default "seq-entry" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:default "seq-align-set" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_ids_filename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . sld:type cwl:Directory . sld:type xsd:boolean . cwl:source , . sld:type cwl:File . sld:type xsd:boolean .