@prefix CommandLineBinding: . @prefix xsd: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix Dirent: . @prefix cwl: . @prefix ResourceRequirement: . @prefix File: . @prefix ExpressionTool: . cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workpath" ] ; sld:default "workpath" ; sld:type xsd:string , sld:null . sld:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type cwl:Directory . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-q_coverage_threshold" ] ; sld:default 9e-01 ; sld:type xsd:float , sld:null . rdfs:label "Run CheckM" ; cwl:in , , , , , , ; cwl:out , ; cwl:run . 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:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; sld:default "protein.seqids" ; sld:type xsd:string . cwl:source . sld:default "nucl" . sld:default true . cwl:source , . sld:default "mapped-aligns.asn" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "asndisc_cpp.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-short-protein-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-short-protein-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-short-protein-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-short-protein-threshold" ] ; sld:type xsd:int , sld:null . rdfs:label "Find Best Evidence Alignments" ; cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-wp-hashes" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.submit_block_name )" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; sld:type xsd:string , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.plasmid_orfs_out)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . sld:default 200 . sld:type cwl:Directory . sld:default "all-proteins.ids" . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "prot.seq_ids" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:boolean . sld:default 1 . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default 120 . sld:default "query subject" . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-tRNAscan-lib" ] ; sld:default "/netmnt/vast01/gp/ThirdParty/tRNAscan-SE/production/lib" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-outdisc" ] ; sld:default "annot.disc" ; sld:type xsd:string . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "align.asn" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "seqids.mft" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-serial" ] ; sld:type xsd:string , sld:null . cwl:source , . sld:type cwl:File , sld:null . cwl:in , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-submit-block" ] ; sld:default "submit_block_template.asn" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-P" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output-23S" ] ; sld:default "23S.asn" ; sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:boolean . sld:default "seq-align" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-exclude-asndisc-codes" ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-T" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:float , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:label "AntiFam tainted proteins I" ; cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "checkm_wnode" ) ; 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 "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.seqids)" ] ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "models.asn" ; sld:type xsd:string . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.masked_locs_name)" ] ; sld:type cwl:File . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, scatter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . sld:default "*" . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:Directory . cwl:source . sld:type cwl:File . 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 ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--additional-suffix=" ; CommandLineBinding:separate false ] ; sld:default ".xml" ; sld:type sld:null , xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "fscr_calls_pass1" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "fscr_calls_pass1" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# input.mft created for fscr_calls_pass1 from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "input.mft" ] ] . cwl:in , ; cwl:out ; cwl:run . sld:default "remap_align.asn" . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:linkMerge "merge_flattened" ; cwl:source , , . sld:default "fasta_cds_na" . cwl:source , . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-uniquify" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-uniquify" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:source . sld:default "seq-align-set" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_asn_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_asn_name)" ] ; sld:type cwl:File . sld:default true . cwl:source . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_taxid_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-dbname" ] ; sld:default "extdb" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . sld:default "all-proteins.ids" . 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:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch (Rfam rRNA), scatter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . rdfs:label "Run GeneMark (genemark_post)" ; cwl:in , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-accept-align" ] ; sld:default "accept-align.asn" ; sld:type xsd:string . sld:type cwl:File , sld:null . sld:default -1 . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-hfmt" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfull_name)" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "pinger" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "pinger.sh" ) ; cwl:baseCommand ( "pinger.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:stdout "pinger.out" . sld:default false . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_16S_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "fastaval.xml" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-species-genome-size" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-partial-cov-threshold" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "gc_get_molecules" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gc_get_molecules" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs . sld:default "proteins.fa" . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "jobs.xml" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-non-match-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-non-match-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-non-match-output" ] ; sld:default "align-nomatch.asn" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-E" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File . cwl:source . sld:default "query,subject,-score,-num_ident,query_align_len,subject_align_len,query_start,subject_start" . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-pathogen-mode" ] ; sld:default true ; sld:type xsd:boolean , sld:null . a cwl:Workflow ; rdfs:label "protein_extract" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oname)" ] ; sld:type cwl:File . rdfs:label "parameter to store the literal 'blast_rules_db'" ; sld:default "blast_rules_db" ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-text-only" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "orhologous.nucleotide.asn" . a cwl:CommandLineTool ; rdfs:label "identify_wp" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "identify_wp" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , , ; cwl:stderr "application.log" ; cwl:stdout "application.out" . a cwl:Workflow ; rdfs:label "gcaccess_from_list" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "univec_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "univec_wnode" ) ; 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 "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:source . sld:type cwl:Directory . cwl:in , , , , , , ; cwl:out ; cwl:run . sld:type cwl:File . 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 "-nogenbank" ] ; sld:type xsd:boolean . cwl:source . sld:type cwl:Directory , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-subject-allowlist" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subject-allowlist" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subject-allowlist" ] ; sld:default "subject_allowlist.mft" ; sld:type xsd:string , sld:null . cwl:in , , , , , ; cwl:out , , ; cwl:run . sld:default true . cwl:source . sld:type cwl:File . sld:type xsd:int . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-alignments" ] ; sld:default "alignments.mft" ; sld:type xsd:string . sld:type xsd:int . cwl:source . rdfs:label "Resolve Annotation Conflicts" ; cwl:in , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . sld:type cwl:File . sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; sld:type xsd:int , sld:null . sld:default 1e-01 . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-plasmid_orfs" ] ; sld:default "plasmid_orf.ids" ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; sld:type cwl:File . sld:type cwl:Directory . sld:type cwl:File . sld:type cwl:Directory . a cwl:Workflow ; rdfs:label "Execute CRISPR" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-in" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . sld:default 1e-01 . cwl:inputBinding [ CommandLineBinding:prefix "-outdiscxml" ] ; sld:default "annot.disc.xml" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-ostruc" ] ; sld:default "struct.tar.gz" ; sld:type xsd:string , sld:null . sld:default true . sld:type cwl:File . rdfs:label "generate_fscr_feats" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:Directory . sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . sld:default 10000 . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-partial-len-threshold" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:source . sld:default true . rdfs:label "Prepare_Unannotated_Sequences/plasmids" ; sld:type cwl:File . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-xslt-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-mask" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . sld:default "asn-seq-entry" . cwl:source . rdfs:label "AntiFam tainted proteins I/oseqids" ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "foreign_screening" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-val-res-den-xml" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-non-match-output" ] ; sld:default "align-nomatch.asn" ; sld:type xsd:string , sld:null . sld:default true . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:source . cwl:source . sld:type xsd:int . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-outent" ] ; sld:default "annot.ent" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; 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 . sld:type xsd:string . sld:type xsd:int . sld:default "no" . cwl:source . a cwl:CommandLineTool ; rdfs:label "Post-process CMsearch annotations" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unique" "-nogenbank" ) ; cwl:baseCommand ( "annot_merge" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "calls.tab" ; sld:type xsd:string . sld:default 200 . sld:type cwl:Directory . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:default "checkm.LDS2" . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch, execution" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" "-use-alignment-output" "-rfam-version" "15.0" ) ; cwl:arguments ( "-nogenbank" "-use-alignment-output" "-rfam-version" "15.0" ) ; cwl:arguments ( "-nogenbank" "-use-alignment-output" "-rfam-version" "15.0" ) ; cwl:baseCommand ( "cmsearch_wnode" ) ; cwl:baseCommand ( "cmsearch_wnode" ) ; cwl:baseCommand ( "cmsearch_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:in , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , ; cwl:run . sld:type cwl:File . sld:default "pgap" . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:default "annotation.mft" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "align.asn" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:loadContents true ; cwl:source . cwl:source . sld:type cwl:Directory . rdfs:comment "The default: setting is for standard call of pgap.cwl (for example, from pgap.py)" ; sld:default "//*[\n ( @severity=\"ERROR\" or @severity=\"REJECT\" )\n and not(contains(@code, \"GENERIC_MissingPubRequirement\")) \n and not(contains(@code, \"SEQ_DESCR_ChromosomeLocation\")) \n and not(contains(@code, \"SEQ_DESCR_MissingLineage\")) \n and not(contains(@code, \"SEQ_DESCR_NoTaxonID\")) \n and not(contains(@code, \"SEQ_DESCR_OrganismIsUndefinedSpecies\"))\n and not(contains(@code, \"SEQ_DESCR_StrainWithEnvironSample\"))\n and not(contains(@code, \"SEQ_DESCR_BacteriaMissingSourceQualifier\"))\n and not(contains(@code, \"SEQ_DESCR_UnwantedCompleteFlag\")) \n and not(contains(@code, \"SEQ_FEAT_BadCharInAuthorLastName\")) \n and not(contains(@code, \"SEQ_FEAT_ShortIntron\")) \n and not(contains(@code, \"SEQ_INST_InternalNsInSeqRaw\")) \n and not(contains(@code, \"SEQ_INST_ProteinsHaveGeneralID\")) \n and not(contains(@code, \"SEQ_PKG_NucProtProblem\")) \n and not(contains(@code, \"SEQ_PKG_ComponentMissingTitle\")) \n]\n" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "/netmnt/vast01/gp/ThirdParty/GeneMark/" . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "output.asn" ; sld:type sld:null , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:default "seq-align-set" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:default "JSON" ; sld:type xsd:string . 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:inputBinding [ CommandLineBinding:prefix "-gc-cache" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ; cwl:valueFrom "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-only-those-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-only-those-ids" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-submit-block-template" ] ; sld:default "submit_block_template.mft" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "miniprot" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-p" "0.01" "--outs" "0.01" "--outc" "0.01" "-S" "-L" "15" "-n" "2" "-N" "1000" "-t" "16" ) ; cwl:baseCommand ( "miniprot" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:stdout "$(inputs.stdout_redir)" . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . 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:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:baseCommand ( "protein_extract" ) ; cwl:inputs , , , , , ; cwl:outputs , , ] . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-align-fmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-align-fmt" ] ; sld:type xsd:string . 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 "-out" ] ; sld:default "preliminary-models.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-other-assignments" ] ; sld:default "other_assignments.mft" ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "genemark" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "genemark" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${ var blob = '# annotation.mft created for genemark from input annotation File\\n'; if ( inputs.annotation == null ) { return blob; } else { return blob + inputs.annotation.path; } }" ; cwl:entryname "annotation.mft" ] ; cwl:listing [ cwl:entry "${ var blob = '# alignments.mft created for genemark from input alignments File\\n'; if ( inputs.alignments == null ) { return blob; } else { return blob + inputs.alignments.path; } }" ; cwl:entryname "alignments.mft" ] ; cwl:listing [ cwl:entry "${ var blob = '# sequences.mft created for genemark from input sequences File\\n'; if ( inputs.sequences == null) { return blob; } else { return blob + inputs.sequences.path; } }" ; cwl:entryname "sequences.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "assembly.molecules.ids" ; sld:type xsd:string , sld:null . sld:type cwl:Directory . sld:default 21 . cwl:inputBinding [ CommandLineBinding:prefix "-prot_hits" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . sld:type cwl:File . rdfs:label "Convert final protein seqid list to XML jobs" ; cwl:in , ; cwl:out , ; cwl:run . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "propagated_gene_symbols_annot.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-out-product-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-out-product-ids" ] ; sld:default "all-proteins.ids" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.asn_cache.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.asn_cache.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.asn_cache.basename)" ] ; sld:type cwl:Directory . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . rdfs:label "goes to protein_alignment/Seed Search Compartments/compartments" ; cwl:outputSource ; sld:type cwl:File . sld:default true . a cwl:ExpressionTool ; rdfs:label "Split input directory into subpath flows" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var r = {};\n if(inputs.data != null) {\n var l = inputs.data.listing;\n var n = l.length;\n for (var i = 0; i < n; i++) {\n switch (l[i].basename) {\n case 'blast_hits.sqlite':\n r['blast_hits_cache'] = l[i];\n break;\n case 'genus-list':\n r['genus_list'] = l[i];\n break;\n }\n }\n }\n else {\n r['blast_hits_cache'] = r['genus_list'] = null;\n }\n return r;\n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; rdfs:label "compute_gencode" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "compute_gencode" ) ; cwl:baseCommand ( "compute_gencode" ) ; cwl:baseCommand ( "compute_gencode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-models" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-operation" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-operation" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-operation" ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "xmlformat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "" ; cwl:entryname "empty" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-orf_entries" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-marked-annotation" ] ; sld:type xsd:string , sld:null . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ; cwl:valueFrom "${ if( inputs.seq_submit != null ) {return 'seq-submit'; } else { return 'seq-entry'; } }" ] ; sld:default "/dev/null" ; sld:type xsd:string . sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output-seqids" ] ; sld:default "annotation.seqids" ; sld:type xsd:string , sld:null . 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# annots1.mft created for find_orthologs from input annots1 File\\n'; if(inputs.annots1 != null) { blob += inputs.annots1.path + '\\n'; } return blob; }" ; cwl:entryname "annots1.mft" ] ] . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tmp)/$(inputs.out_hmm_params_name)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-reblast-locs" ] ; sld:default "reblast_locs.asn" ; sld:type xsd:string . cwl:source . sld:type xsd:string . sld:default 29 . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.delta_seqs_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.delta_seqs_name)" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "final_bact_asn" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "final_bact_asn" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# cleaned-annotation.mft created for final_bact_asn from input annotation Array of Files\\n'; for (var i = 0; i < inputs.annotation.length; i++) { blob += inputs.annotation[i].path + '\\n'; } return blob; }" ; cwl:entryname "cleaned-annotation.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:default 1e-04 . rdfs:label "Extract Orthologous Prokaryotic Proteins" ; cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . rdfs:label "goes to protein_alignment/Seed Search Compartments/compartments" ; cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Seed Protein Alignments" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . sld:default true ; sld:type xsd:boolean , sld:null . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outname)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-query-allowlist" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-query-allowlist" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-query-allowlist" ] ; sld:default "query_allowlist.mft" ; sld:type xsd:string , sld:null . sld:default true . rdfs:label "Remove off-frame ORFs" ; cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "preliminary-models.asn" ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source , . rdfs:label "align_find_frequent_sas" ; cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "prot.ids" ; sld:type xsd:string , sld:null . cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "annots.asn" ; sld:type xsd:string , sld:null . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-drop-partial-in-the-middle" ] ; sld:type xsd:boolean , sld:null . sld:default "prot" . sld:default true . cwl:source . cwl:source . cwl:source . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-orfs-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-orfs-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-orfs-manifest" ] ; sld:default "ids.mft" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; 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:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output-5S" ] ; sld:default "5S.asn" ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-xslt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt" ] ; sld:type cwl:File , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "Seed Protein Alignments, gather" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unzip" "*" "-num-partitions" "1" ) ; cwl:baseCommand ( "gpx_make_outputs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:source . cwl:source . cwl:source . sld:type cwl:File . rdfs:comment "corresponds to bacterial_screening plane in in foreign contamination screening graph of classic Gpipe" ; rdfs:label "bacterial_screening" ; cwl:in , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_output)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; sld:type cwl:File . rdfs:label "Prepare Annotation Input" ; cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:source . sld:default "F" . cwl:inputBinding [ CommandLineBinding:prefix "-x" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "xml_evaluate" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "xml_evaluate" ) ; cwl:baseCommand ( "xml_evaluate" ) ; cwl:baseCommand ( "xml_evaluate" ) ; cwl:baseCommand ( "xml_evaluate" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.stdout_redir)" . cwl:source . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; sld:default "var_proc_annot_stats.val.xml" ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . sld:default "models.asn" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_report)" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_23S_name)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-m" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-start-stop-allowance" ] ; sld:type xsd:int , sld:null . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string . sld:default "PGAP" . a cwl:CommandLineTool ; rdfs:label "genemark_training" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "genemark" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; 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 = '# 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 "${ var blob = '# alignments.mft created for genemark_training from input alignments File\\n'; if ( inputs.alignments == null ) { return blob; } else { return blob + inputs.alignments.path; } }" ; cwl:entryname "alignments.mft" ] ] . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Check for internal N's" ; cwl:inputBinding [ CommandLineBinding:prefix "-check_internal_ns" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:default "proteins-for-checkm.asn" . rdfs:label "PGAP Pipeline" ; cwl:in , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , ; cwl:run . rdfs:label "PGAP + ab initio" ; cwl:in , ; cwl:out ; cwl:run . cwl:source , . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-selenoproteins" ; cwl:valueFrom "$(inputs.selenoproteins.path)/$(inputs.selenoproteins_db)" ] ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "Bacterial Annotation, ab initio (first pass) searched against AntiFam" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-e" ] ; sld:type xsd:string , sld:null . cwl:source , . sld:default "seq-entry" . sld:default 0 . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:default "annotation.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.output_db_file)" ] ; sld:type xsd:string . sld:default 180 . a cwl:CommandLineTool ; rdfs:label "Filter Protein Alignments" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-filter" "query_subject_overlap < 10 AND pct_identity_gapopen_only >= 50 AND NOT (pct_coverage < 20 and (query_entropy < 0.3 OR query_seg_pct > 60)) AND ( (query_start<=20 AND SUB(query_length, query_end)<=20) OR pct_identity_gapopen_only >= 60 ) AND (SUB(subject_end, subject_start) > 90 OR SUB(subject_end, subject_start) > MUL(query_length,1.5) OR num_ident >=60) AND (query_length > 30 OR (pct_identity_gap >= 80 AND SUB(subject_end, subject_start) >= MUL(query_length,2.4)))" "-ifmt" "seq-align" "-nogenbank" ) ; cwl:baseCommand ( "align_filter" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.uniColl_asn_cache)" ] ] . cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.jobs_name)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "miniprot.asn" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "paf2asn" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-partial-intron-threshold" "100" "-no-scores" "-pack-parts" "-split-introns" "-uniquify" ) ; cwl:baseCommand ( "paf2asn" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# paf.mft created for paf2asn from input paf Array of Files\\n'; for (var i = 0; i < inputs.paf.length; i++) { blob += inputs.paf[i].path + '\\n'; } return blob; }" ; cwl:entryname "paf.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-gc2" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "yaml2json" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "yaml2json.py" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-prok-entrez-gene-stuff" ] ; sld:default "prok_entrez_gene_stuff.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-action" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-action" ] ; sld:type xsd:string . cwl:source . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.precedence_filename)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "submol.json" ; sld:type xsd:string . sld:type xsd:string . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . sld:default 50 . rdfs:label "ab initio AntiFam tainted proteins" ; cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . sld:default "yes" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preliminary_models_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . rdfs:label "Cache Entrez Gene" ; cwl:in , , , ; cwl:out ; cwl:run . sld:default "var_proc_annot_stats.disc.xml" . cwl:source . sld:type xsd:int . sld:default "create" . cwl:source . a cwl:CommandLineTool ; rdfs:label "file concatenation" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:stdout "cat.out" . sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "bacterial_hit_mapping" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bacterial_hit_mapping" ) ; cwl:baseCommand ( "bacterial_hit_mapping" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${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:ResourceRequirement ; ResourceRequirement:ramMax 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# aligns.mft created for bacterial_hit_mapping from input hmm_hits Array of Files\\n'; for (var i = 0; i < inputs.hmm_hits.length; i++) { blob += inputs.hmm_hits[i].path + '\\n'; } return blob; }" ; cwl:entryname "aligns.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:default true ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "calls.asn" ; sld:type xsd:string . sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:Directory . sld:type xsd:int . cwl:in , ; cwl:out , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "entries.asn" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-oreport" ] ; sld:default "report.tsv" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-oasn" ] ; sld:default "trnascan.asn" ; sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sequences_name)" ] ; sld:type cwl:File . cwl:in , ; cwl:out , , ; cwl:run . sld:default 60 . cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; sld:default "blastdb" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-label-suffix" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-label-suffix" ] ; sld:type xsd:string . sld:type xsd:boolean . cwl:source . sld:default false . cwl:source . cwl:in , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) . rdfs:label "BLASTp Current Prokaryotic Proteins vs Orthologs/cat aligns" ; cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; 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 . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-offset" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-offset" ] ; sld:type xsd:long , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:source . sld:type cwl:Directory . sld:default "subject" . sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . sld:default "## FASTA" ; sld:type xsd:string , sld:null . rdfs:comment "FASTA file with user provided headers and user provided prokaryota genome" ; cwl:inputBinding [ CommandLineBinding:prefix "-input-fasta" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-pgap-details" ] ; sld:default "var_bact_univ_prot_details.xml" ; sld:type xsd:string . cwl:source . rdfs:label "Get Proteins" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-files-per-dir" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-files-per-dir" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-T" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default true . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; sld:default 1e-02 ; sld:type xsd:float , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "cmsearch.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-no-internet" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:default 180 . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-U" ] ; sld:type xsd:boolean , sld:null . sld:default true . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-f" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; 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 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-locus-tag-prefix" ] ; sld:default "pgaptmp_" ; sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . sld:default false . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-annot" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-genemark-annot" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "concatenates input File[] to screen" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . rdfs:label "Create Orthologous Prokaryotic Protein BLASTdb" ; cwl:in , , , ; cwl:out ; cwl:run . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-max-objects" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-objects" ] ; sld:type xsd:int , sld:null . sld:default "seq-annot" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.reblast_locs_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; 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:source . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:default 5e-02 . cwl:source . sld:default 1e-01 . cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; sld:default "subject" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-P" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; sld:default 250 ; sld:type xsd:int , sld:null . sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:default 20 . cwl:source . sld:default "query,subject,-score,cigar" . sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-no-internet" ] ; sld:type xsd:boolean , sld:null . a cwl:Workflow ; rdfs:label "vecscreen" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nuc_fasta_name)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "" ; rdfs:label "prepare_seq_entry_input" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "prepare_seq_entry_input" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:label "pgapx_yaml_ctl" ; cwl:in , , , , ; cwl:out , , , ; cwl:run . cwl:source . cwl:in ; cwl:out , ; cwl:run . sld:type cwl:File . rdfs:label "Bacterial Annot Filter" ; cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subjects-gc-id-list" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_glob)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "sqn2gbent" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "sqn2gbent" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:source . rdfs:label "Extract final proteins" ; cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type sld:null , xsd:boolean . cwl:source , . cwl:source . a cwl:Workflow ; rdfs:label "checkm_wnode" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , . a cwl:CommandLineTool ; rdfs:label "Seed Protein Alignments, execute" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-align_filter" "pct_identity_gapopen_only >= 75" "-backlog" "1" "-comp_based_stats" "F" "-dbsize" "6000000000" "-delay" "0" "-evalue" "0.1" "-gapextend" "2" "-gapopen" "9" "-matrix" "BLOSUM62" "-max-jobs" "1" "-seg" "no" "-soft_masking" "true" "-threshold" "21" "-word_size" "6" "-nogenbank" "-short-protein-threshold" "30" ) ; cwl:baseCommand ( "tblastn_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 "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.uniColl_asn_cache)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 4000 ] . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ingb" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File , sld:null . sld:default "subject" . a cwl:CommandLineTool ; rdfs:label "seq_filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-filter" "length < 30" ) ; cwl:baseCommand ( "seq_filter" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# seqids.mft created for seq_filter from input seqids Array of Files\\n'; for (var i = 0; i < inputs.seqids.length; i++) { blob += inputs.seqids[i].path + '\\n'; } return blob; }" ; cwl:entryname "seqids.mft" ] ] . cwl:source . sld:default 15000000 . cwl:inputBinding [ CommandLineBinding:prefix "-output-asn-type" ] ; sld:default "input_asn_type.txt" ; sld:type xsd:string . rdfs:label "BLASTp Current Prokaryotic Proteins vs Orthologs" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default "annot.fna" . cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-olds2" ] ; 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:source . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "sparclbl" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "sparclbl_mp.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 15000 ] . cwl:inputBinding [ CommandLineBinding:prefix "-superkingdom" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-superkingdom" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-superkingdom" ] ; sld:type xsd:boolean , sld:null . sld:default "-" . sld:type xsd:int . sld:default "seq-entry" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.ostruct)" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out , , , , , , ; cwl:run . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:type cwl:Directory . sld:type cwl:Directory , sld:null . cwl:source . cwl:source . cwl:source . sld:default "annot.faa" . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . sld:default "yes" . sld:default true . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:source . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:default true . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-A" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_seqids_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; 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 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:source . sld:default 1 . a cwl:Workflow ; rdfs:label "Run tRNAScan" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-title" ] ; sld:type xsd:string . rdfs:label "Find best protein hits" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-submit-block-template" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-submit-block-template" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:default "stop" . cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-op" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type xsd:string . cwl:source . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch (5S rRNA), scatter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "get_orthologous_assembly" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "get_orthologous_assembly" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-sra-acc" ] ; sld:type xsd:string , sld:null . sld:default "remap" . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "screen_evaluate" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "screen_evaluate" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . sld:default 5000 . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "The default: setting is for standard call of pgap.cwl (for example, from pgap.py)" ; sld:default "//*[@severity=\"FATAL\"]" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output-manifest" ] ; 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 . cwl:source . sld:type cwl:File . cwl:source . sld:default 1.5e-01 . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 3 ; CommandLineBinding:prefix "state" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 3 ; CommandLineBinding:prefix "state" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-calls" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-aligns" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . 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:inputBinding [ CommandLineBinding:prefix "-b" ; cwl:valueFrom "$(inputs.b.path)/$(inputs.blastdb)" ] ; sld:default "cdd" ; sld:type xsd:string . sld:type xsd:string . sld:default "hmm_hits.asn" . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "gencoll.asn" ; sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, transform" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-X" "20" ) ; cwl:baseCommand ( "trnascan_dump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , . a cwl:Workflow ; rdfs:label "tt_blastn_wnode" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . a cwl:CommandLineTool ; rdfs:label "asnvalidate" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asnvalidate" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "bact_annot_filter" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bact_annot_filter" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# annotation.mft created for bact_annot_filter.mft from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "annotation.mft" ] ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gpx_qdump" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:arguments ( "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnb" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "hmm-assignments.xml" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . sld:default true . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . sld:default 250 . sld:type cwl:Directory . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:in , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . cwl:source . sld:default true . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:default true . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:in , ; cwl:out , ; cwl:run [ a cwl:ExpressionTool ; ExpressionTool:expression "${ if ( inputs.input_asn_type == 'seq-entry' ) { return { 'output_entries': inputs.input, 'output_seq_submit': null } } if ( inputs.input_asn_type == 'seq-submit' ) { return { 'output_entries': null, 'output_seq_submit': inputs.input } } }" ; cwl:inputs , ; cwl:outputs , ] . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "best_aligns.asn" ; sld:type xsd:string . cwl:source . sld:type xsd:string , sld:null . rdfs:comment "this parameter is fixed for this command line workflow, because the output is defined as single file\n" ; cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; sld:default 1 ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "protein_assignments.xml" ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.workpath)" ] ; sld:type cwl:Directory . sld:default true . sld:default "sequences.text.asn" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . sld:type xsd:int . sld:default "subject_coverage >= 10" . cwl:inputBinding [ CommandLineBinding:prefix "-feats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-feats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-feats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-feats" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-feats" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-compartments-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-compartments-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-compartments-manifest" ] ; sld:default "compartments.mft" ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "Bacterial Annotation, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . cwl:outputSource ; sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_non_match)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:default "separator.txt" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-sra-file" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-submission-mode-genbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-mask" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output-ltp" ] ; sld:default "genome.ltp.txt" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; sld:type xsd:string . sld:default "contam_in_prok" . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out ; cwl:run [ a cwl:CommandLineTool ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; cwl:baseCommand ( "gp_makeblastdb" ) ; 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)" ] ] ; 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)" ] ] ; 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 [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:default "concatenated.file" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-aligns-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-aligns-manifest" ] ; sld:default "aligns.mft" ; sld:type xsd:string , sld:null . cwl:source . sld:default "fasta_cds_aa" . rdfs:label "Get List of Order Specific Databases in the form of string[]" ; cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_orthologs)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "cleaned-annotation.asn" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "set_operation" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "set_operation" ) ; cwl:baseCommand ( "set_operation" ) ; cwl:baseCommand ( "set_operation" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# A.mft created for set_operation from input A Array of Files\\n'; for (var i = 0; i < inputs.A.length; i++) { blob += inputs.A[i].path + '\\n'; } return blob; }" ; cwl:entryname "A.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# B.mft created for set_operation from input B Array of Files\\n'; for (var i = 0; i < inputs.B.length; i++) { blob += inputs.B[i].path + '\\n'; } return blob; }" ; cwl:entryname "B.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# A.mft created for set_operation from input A Array of Files\\n'; for (var i = 0; i < inputs.A.length; i++) { blob += inputs.A[i].path + '\\n'; } return blob; }" ; cwl:entryname "A.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# B.mft created for set_operation from input B Array of Files\\n'; for (var i = 0; i < inputs.B.length; i++) { blob += inputs.B[i].path + '\\n'; } return blob; }" ; cwl:entryname "B.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# B.mft created for set_operation from input B Array of Files\\n'; for (var i = 0; i < inputs.B.length; i++) { blob += inputs.B[i].path + '\\n'; } return blob; }" ; cwl:entryname "B.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# A.mft created for set_operation from input A Array of Files\\n'; for (var i = 0; i < inputs.A.length; i++) { blob += inputs.A[i].path + '\\n'; } return blob; }" ; cwl:entryname "A.mft" ] ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . sld:default ; sld:type cwl:Directory . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type xsd:boolean , sld:null . sld:default "-" . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output-manifest" ] ; sld:default "blastdb.mft" ; sld:type xsd:string . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "cluster_blastp_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cluster_blastp_wnode" ) ; cwl:baseCommand ( "cluster_blastp_wnode" ) ; cwl:baseCommand ( "cluster_blastp_wnode" ) ; cwl:baseCommand ( "cluster_blastp_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.lds2)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 5000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.lds2)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 5000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 5000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 true ; cwl:entry "$(inputs.lds2)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable true ; cwl:entry "$(inputs.lds2)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 5000 ] . a cwl:Workflow ; rdfs:comment "Prepare user input for NCBI-PGAP pipeline" ; rdfs:label "Prepare user input" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:default "stdout" ; sld:type xsd:string , sld:null . 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:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "mkdir $(inputs.blastdir) && cp" ] ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; sld:default "all" ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-db" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default false . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . sld:type cwl:Directory . sld:type cwl:Directory . sld:type cwl:Directory . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "out-annotation.asn" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:label "orf_hits_cache_retrieve" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "orf_hits_cache_retrieve" ) ; cwl:baseCommand ( "orf_hits_cache_retrieve" ) ; cwl:baseCommand ( "orf_hits_cache_retrieve" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${\n var blob = '# ids.mft created for orf_hits_cache_retrieve from input \"orfs\" Array of Files' +\n String.fromCharCode(10) ; \n for (var i = 0; i < inputs.orfs.length; i++) { \n blob += inputs.orfs[i].path + String.fromCharCode(10); \n } \n return blob; \n}" ; cwl:entryname "ids.mft" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${\n var blob = '# ids.mft created for orf_hits_cache_retrieve from input \"orfs\" Array of Files' +\n String.fromCharCode(10) ; \n for (var i = 0; i < inputs.orfs.length; i++) { \n blob += inputs.orfs[i].path + String.fromCharCode(10); \n } \n return blob; \n}" ; cwl:entryname "ids.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${\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:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:default "blastdb" . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "fscr_format_calls" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" "-no-taxon-access" ) ; cwl:baseCommand ( "fscr_format_calls" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . sld:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; sld:default false ; sld:type xsd:boolean , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-defline-cleanup-rules" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-rfam-stockholm" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch (Rfam rRNA), gather" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unzip" "*" "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . sld:default "blastdb" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${ return { \"value\": String(inputs.input.contents).trim() }; }\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "Post-process CMsearch annotations" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unique" "-nogenbank" ) ; cwl:arguments ( "-unique" "-nogenbank" ) ; cwl:arguments ( "-unique" "-nogenbank" ) ; cwl:baseCommand ( "annot_merge" ) ; cwl:baseCommand ( "annot_merge" ) ; cwl:baseCommand ( "annot_merge" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-seg" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . sld:default "seq-align" . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assm-name" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "$(inputs.blastdb_dir.path)/$(inputs.blastdb)" ] ; sld:default "blastdb" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "$(inputs.gc_assm_name.basename)" . cwl:inputBinding [ CommandLineBinding:prefix "-check_exome" ] ; sld:default true ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "ncbi_crispr.out" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-perc_identity" ] ; sld:type xsd:float , sld:null . cwl:source . sld:type cwl:Directory , sld:null . sld:type xsd:string . rdfs:label "Add Checksum to Genbank class ENT" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; sld:type xsd:boolean . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:source . rdfs:comment "Base path to files of output generated from processes" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch (5S rRNA), gather" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unzip" "*" "-produce-empty-file" ) ; cwl:arguments ( "-unzip" "*" "-produce-empty-file" ) ; cwl:arguments ( "-unzip" "*" "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "annot.gbk" ; sld:type xsd:string . sld:type cwl:Directory . cwl:source . sld:type cwl:File . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:default true . sld:default "6000000000" . cwl:source . cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.var_bact_univ_prot_details_xml_name)" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . rdfs:label "Map Naming Hits" ; cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "application.log" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . sld:type cwl:Directory . rdfs:label "Prepare user input" ; cwl:in , , , , ; cwl:out , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . 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 . a cwl:CommandLineTool ; rdfs:label "Seed Protein Alignments, scatter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-affinity" "subject" "-max-batch-length" "10000" "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.uniColl_asn_cache)" ] ] . cwl:outputSource , ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default true . a cwl:Workflow ; rdfs:comment "PGAP pipeline for external usage, powered via containers" ; rdfs:label "PGAP Pipeline" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bact_filter_orfs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-long-orf-thresh" "450" "-include-uncovered-regions" "-include-overlap-regions" ) ; cwl:baseCommand ( "bact_filter_orfs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , . cwl:source . sld:default 50 . 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:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . sld:default "predicted-protein" . sld:type cwl:File . cwl:source . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "trnascan_wnode and gpx_qdump combined" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs . rdfs:label "Extract ORF Proteins/lds2" ; sld:type cwl:File . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var values=[];\n var lines=[];\n if(inputs.input != null) {\n lines = inputs.input.contents.split(\"\\n\");\n }\n for(var i = 0; i-1) {\n basename = basename.substr(last_slash_i + 1).trim();\n }\n if(basename.length > 0) {\n values.push (basename);\n }\n }\n return { \"values\": values }; \n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.mask)?*$(inputs.suffix)" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-input-16S" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-excluded-seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-excluded-seqs" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:source . sld:default true . cwl:source , . cwl:source . sld:default 21 . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-pgap-output" ] ; sld:default "var_proc_annot_stats.xml" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type cwl:File , sld:null . rdfs:label "align_filter" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-group" ] ; sld:type xsd:int , sld:null . sld:default "BLASTdb created by GPipe" . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:default true . sld:type cwl:File . rdfs:label "Name by WPs" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-class" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-class" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "annot_checksum.asn" ; sld:type xsd:string , sld:null . sld:default 5000 . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-master-desc" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string . rdfs:label "AntiFam tainted proteins" ; cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . sld:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-items-per-chunk" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-items-per-chunk" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-seqids" ] ; sld:type cwl:File . cwl:source . sld:default "seq-align" . cwl:inputBinding [ CommandLineBinding:prefix "-n" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "separate_plasmid_orfs" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "separate_plasmid_orfs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . sld:default true . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-minsize" ] ; sld:default 42 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.O)" ] ; sld:type cwl:Directory . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.marked_annotation_name)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . sld:default "annot-gb-wo-checksum.ent" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_output)" ] ; sld:type cwl:File . sld:type cwl:Directory . cwl:source . rdfs:label "Search AntiFam I" ; cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:Directory . rdfs:label "Run GeneMark Training, genemark" ; cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-n l//" ; CommandLineBinding:separate false ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . sld:default "pgap" . sld:default "30 2.2 2.5" . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . sld:default "asn-binary" . sld:default [ a cwl:File ; File:contents "" ; cwl:basename "null" ; cwl:path ] . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:default "vector" . rdfs:label "Find Naming Protein Hits" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source , , , , , . cwl:linkMerge "merge_flattened" ; cwl:source , . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${ return { \"value\": parseInt(inputs.input.contents) }; }\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-a" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Run genomic CMsearch (Rfam rRNA), execution" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" "-rfam-version" "15.0" ) ; cwl:baseCommand ( "cmsearch_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . sld:default "*" . rdfs:label "Add Checksum to SQN" ; cwl:in , , , , ; cwl:out ; cwl:run . sld:default "score>0 && pct_identity_gapopen_only > 35" . sld:default "all" . cwl:source . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . rdfs:label "prime_cache" ; cwl:in ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "assembly.report.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-d" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-min_seq_len" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:default true . cwl:source . cwl:source . rdfs:label "Extract Model Proteins" ; cwl:in , ; cwl:out , , ; cwl:run . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cache_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cache_dir)" ] ; sld:type cwl:Directory . sld:type cwl:Directory , sld:null . a cwl:CommandLineTool ; rdfs:label "gp_fetch_sequences" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_fetch_sequences" ) ; 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 "$(inputs.proteins)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-o_stats" ] ; sld:default "stats.xml" ; sld:type xsd:string , sld:null . sld:type xsd:boolean . cwl:source . sld:default 5e-01 . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "vector" . sld:default "*" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.preliminary_models_name)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pinger.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "pinger.out" ] ; sld:type cwl:File . sld:default "blast_rules_db" . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-raw_seqs" ] ; sld:type cwl:File . sld:default "OVERLAPPING_GENES" , "MISSING_AFFIL" , "COMMENT_PRESENT" , "OVERLAPPING_CDS" , "BAD_LOCUS_TAG_FORMAT" , "PARTIAL_CDS_COMPLETE_SEQUENCE" , "EXTRA_GENES" , "SHORT_PROT_SEQUENCES" , "FEATURE_LIST" , "FLATFILE_FIND" , "N_RUNS" , "TAX_LOOKUP_MISSING" , "BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS" , "TAX_LOOKUP_MISMATCH" , "AUTODEF_USER_OBJECT" , "BAD_BGPIPE_QUALS" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; sld:type xsd:int , sld:null . sld:type xsd:boolean . sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File , sld:null . sld:type xsd:float , sld:null . cwl:in ; cwl:out , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:run . sld:default 300 . cwl:inputBinding [ CommandLineBinding:prefix "-swap-rows" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-window" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-window" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.olds2)" ] ; sld:type cwl:File . sld:default "annot-gb.ent" . sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "xsltproc" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "xsltproc" ) ; cwl:baseCommand ( "xsltproc" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-dust" ] ; sld:type xsd:string , sld:null . sld:default "final_asnval_diag.xml" . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . sld:type xsd:int . cwl:source . sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bacterial_resolve_conflicts" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "bacterial_resolve_conflicts" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${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:listing [ cwl:entry "${var blob = '# features.mft created for bacterial_resolve_conflicts from input features Array of Files\\n'; if ( ! inputs.hasOwnProperty('features') ) { return blob; }; for (var i = 0; i < inputs.features.length; i++) { blob += inputs.features[i].path + '\\n'; } return blob; }" ; cwl:entryname "features.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "gencode.txt" ; sld:type xsd:string . sld:default 1e-03 . cwl:inputBinding [ CommandLineBinding:prefix "-A" ; cwl:valueFrom "${if (inputs.superkingdom==2157) { return true; } else {return false; } }" ] ; sld:default true ; sld:type xsd:boolean . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-sra-file" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-task" ] ; sld:default "blastn" ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . sld:default "master" . rdfs:label "Prepare_Unannotated_Sequences/sequences" ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.output_entries_name )" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_5S_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-oseq-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseq-ids" ] ; sld:default "oseq-ids.seqids" ; sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "asn_translated.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ouniversal-clusters" ] ; sld:default "universal_clusters.inf" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source , . sld:default "all.gi" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-5S" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-outval" ] ; sld:default "meta.annot.val" ; sld:type xsd:string . rdfs:label "Find Prokaryotic Orthologs" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . sld:default 60 . cwl:in , , ; cwl:out , ; cwl:run . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-source" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-source" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-odelta-seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-odelta-seqs" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . sld:default "no" . sld:type cwl:File . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:source . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "align.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; sld:default true ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.blastdir)" ] ; sld:type cwl:Directory . cwl:source . cwl:source . sld:default 1e-01 . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-repeat-threshold" ] ; sld:type xsd:int , sld:null . rdfs:label "gp_makeblastdb" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:label "Good ab initio proteins" ; cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outent_name)" ] ; sld:type cwl:File . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-proteins" ] ; sld:default "proteins.mft" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "collect_annot_stats" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "collect_annot_stats" ) ; cwl:baseCommand ( "collect_annot_stats" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# proc_annot_stats_or_details.mft created for collect_annot_stats from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "proc_annot_stats_or_details.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# proc_annot_stats_or_details.mft created for collect_annot_stats from input input Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "proc_annot_stats_or_details.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; sld:type cwl:File . sld:default "final_asndisc_diag.xml" . cwl:inputBinding [ CommandLineBinding:prefix "-abs-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-Q" ] ; sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_ltp_name)" ] ; sld:type cwl:File . sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "generate_fscr_feats" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "generate_fscr_feats" ) ; cwl:baseCommand ( "generate_fscr_feats" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "models.asn" ; sld:type xsd:string , sld:null . rdfs:label "Add Names to Proteins" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run [ a cwl:CommandLineTool ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; cwl:baseCommand ( "sqlite3" ) ; 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)" ] ] ; 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)" ] ] ; 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)" ] ] ; 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:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:default "entrez" . sld:type cwl:File , sld:null . sld:type xsd:string , sld:null . sld:default 10000 . cwl:inputBinding [ CommandLineBinding:prefix "-max-size" ] ; sld:type xsd:long . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.L_output)" ] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "bacterial_screening" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type cwl:File . sld:default "BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS" , "PARTIAL_CDS_COMPLETE_SEQUENCE" , "MISSING_AFFIL" , "SHORT_PROT_SEQUENCES" , "FLATFILE_FIND" , "OVERLAPPING_CDS" , "COMMENT_PRESENT" , "AUTODEF_USER_OBJECT" , "TAX_LOOKUP_MISSING" , "EXTRA_GENES" , "OVERLAPPING_GENES" , "N_RUNS" , "TAX_LOOKUP_MISMATCH" , "BAD_BGPIPE_QUALS" , "FEATURE_LIST" . a cwl:Workflow ; rdfs:label "spurious_annot pass2" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:default 5000 . cwl:inputBinding [ CommandLineBinding:prefix "-aligns" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-aligns" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-aligns" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:default true . sld:type cwl:Directory . sld:default true . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-namedb" ; cwl:valueFrom "$(inputs.namedb_dir.path)/$(inputs.namedb)" ] ; sld:type xsd:string , sld:null . sld:default false . sld:default "miniprot_fast.paf" ; sld:type xsd:string , sld:null . sld:default "add" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:Directory . rdfs:comment "JSON file with submission and molecule specification" ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-delay" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:label "Run GeneMark" ; cwl:in , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . rdfs:label "Good, AntiFam filtered proteins" ; cwl:in , , ; cwl:out ; cwl:run . rdfs:label "Extract Orthologous Prokaryotic Proteins: fetch nucleotide ASN.1" ; cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . sld:type cwl:File . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:in , , , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Execute CRISPR, scatter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-batch-size" "1" "-nogenbank" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-sra-acc" ] ; sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . sld:type cwl:Directory . cwl:source . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "annot_checksum" ) ; cwl:baseCommand ( "annot_checksum" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.xml_impl)" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . sld:type xsd:string . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-outfull" ] ; sld:default "annot-full.ent" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int . cwl:source . sld:default "proc_annot_details.xml" . cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; sld:type xsd:string , sld:null . sld:default true . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default "genomic.fa" . cwl:source . cwl:in , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "paf.mft" ; sld:type xsd:string , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-selected-blastdb-manifest" ] ; sld:default "selected_blastdb.mft" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "fscr_feats.asn" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "seq-entry" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-xpath-fail" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-fail" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-fail" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-fail" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-exclude-external" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "asn-binary" . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-output-nomatch" ] ; sld:default "no-match" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "prime_cache" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "prime_cache" ) ; cwl:baseCommand ( "prime_cache" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs , . cwl:source . sld:default "binary" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . sld:default 10 . cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "do_report" ] ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "do_report" ] ; sld:type xsd:boolean . a cwl:Workflow ; rdfs:label "spurious_annot" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outmetamaster_name)" ] ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-univ-prot-xml" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . sld:default 300 . sld:default "var_proc_annot_stats.val.xml" . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-l" ] ; sld:type sld:null , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-gencode" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-gencode" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-gencode" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-path" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-db_gencode" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:type cwl:File . sld:default "t" . sld:default "BLASTdb created by GPipe" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-features" ] ; sld:default "features.mft" ; sld:type xsd:string . cwl:source . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output-16S" ] ; sld:default "16S.asn" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "checkm.txt" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-oseqids" ] ; 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 . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:default 21 . sld:default "annot.sqn" . sld:default "annot_with_genomic_fasta.gff" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-precedences" ] ; sld:default "precedences.tsv" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-indir" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oname)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "align_filter" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "align_filter" ) ; cwl:baseCommand ( "align_filter" ) ; cwl:baseCommand ( "align_filter" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# query_allowlist.mft created for align_filter from input \"query_allowlist\" File\\n'; if ( inputs.query_allowlist == null) { return blob; } else { blob += inputs.query_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "query_allowlist.mft" ] ; cwl:listing [ cwl:entry "${\n var blob = '# compartments.mft created for align_filter from input \"compartments\" Array of Files\\n';\n if (inputs.compartments) { \n for (var i = 0; i < inputs.compartments.length; i++) {\n blob += inputs.compartments[i].path + '\\n';\n }\n }\n return blob;\n}\n" ; cwl:entryname "compartments.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# aligns.mft created for align_filter from input \"input\" Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "aligns.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# subject_allowlist.mft created for align_filter from input \"subject_allowlist\" File\\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "subject_allowlist.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${\n var blob = '# compartments.mft created for align_filter from input \"compartments\" Array of Files\\n';\n if (inputs.compartments) { \n for (var i = 0; i < inputs.compartments.length; i++) {\n blob += inputs.compartments[i].path + '\\n';\n }\n }\n return blob;\n}\n" ; cwl:entryname "compartments.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# query_allowlist.mft created for align_filter from input \"query_allowlist\" File\\n'; if ( inputs.query_allowlist == null) { return blob; } else { blob += inputs.query_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "query_allowlist.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# subject_allowlist.mft created for align_filter from input \"subject_allowlist\" File\\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "subject_allowlist.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# aligns.mft created for align_filter from input \"input\" Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "aligns.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# subject_allowlist.mft created for align_filter from input \"subject_allowlist\" File\\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "subject_allowlist.mft" ] ; cwl:listing [ cwl:entry "${\n var blob = '# compartments.mft created for align_filter from input \"compartments\" Array of Files\\n';\n if (inputs.compartments) { \n for (var i = 0; i < inputs.compartments.length; i++) {\n blob += inputs.compartments[i].path + '\\n';\n }\n }\n return blob;\n}\n" ; cwl:entryname "compartments.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# query_allowlist.mft created for align_filter from input \"query_allowlist\" File\\n'; if ( inputs.query_allowlist == null) { return blob; } else { blob += inputs.query_allowlist.path + '\\n'; return blob; }}" ; cwl:entryname "query_allowlist.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# aligns.mft created for align_filter from input \"input\" Array of Files\\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\\n'; } return blob; }" ; cwl:entryname "aligns.mft" ] ] . cwl:source . sld:default true . cwl:source . cwl:source . sld:default "annot_cds_from_genomic.fna" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oproteins)" ] ; sld:type cwl:File . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gpx_make_outputs" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gpx_make_outputs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-genemark-path" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-input-23S" ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-oall" ] ; sld:default "all_prots.seqid" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-orf_ids" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . sld:type cwl:Directory . cwl:source . cwl:source , . sld:default "sequences.val" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; 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 ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "hmmsearch_create_jobs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:arguments ( "-no-merge-hmms" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:baseCommand ( "hmmsearch_create_jobs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] . cwl:source . sld:default "seq-entry" . cwl:source . sld:default "seq-align-set" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . sld:default 120 . sld:default true . sld:type xsd:string , sld:null . a cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.clust_output)" ] ; sld:type cwl:File . sld:default 0 . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; sld:type xsd:int , sld:null . sld:default "seq-align-set" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:linkMerge "merge_flattened" ; sld:default "blast_rules_db" , "blastdb" . cwl:source . a cwl:Workflow ; rdfs:label "Non-Coding Bacterial Genes" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_input_asn_type_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "Align reference proteins plane complete workflow, with miniprot" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , , , , , , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , , , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-margin" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oseqids_name)" ] ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:int . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fasta" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-params" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-len" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-len" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source , . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-submol_block_json" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "seq-align" . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-gbload" ] ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_annotation_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_annotation_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . sld:default "orf" . cwl:outputSource ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-genbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "jobs.xml" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.models_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.models_name)" ] ; sld:type cwl:File . sld:type xsd:boolean . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "ent2sqn" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "ent2sqn" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# submit_block_template.mft created for ent2sqn from input submit_block_template Array of Files\\n'; for (var i = 0; i < inputs.submit_block_template.length; i++) { blob += inputs.submit_block_template[i].path + '\\n'; } return blob; }" ; cwl:entryname "submit_block_template.mft" ] ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; 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 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . sld:default true . cwl:source . cwl:source . cwl:source , . a cwl:CommandLineTool ; rdfs:label "hmmsearch_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:arguments ( "-backlog" "1" "-cut_ga" "-nogenbank" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:baseCommand ( "hmmsearch_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; 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.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ; cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; 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:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${ var blob = '# fam.mft created for hmmsearch_wnode from input hmms_tab File\\n'; if ( inputs.hmms_tab == null ) { return blob; } else { return blob + inputs.hmms_tab.path; } }" ; cwl:entryname "fam.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.workdir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.hmm_path)" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 3000 ] . a cwl:CommandLineTool ; rdfs:label "std_validation" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "std_validation" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# submit_block_template.mft created for std_validation from input submit_block_template Array of Files\\n'; for (var i = 0; i < inputs.submit_block_template.length; i++) { blob += inputs.submit_block_template[i].path + '\\n'; } return blob; }" ; cwl:entryname "submit_block_template.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# master_desc_mft.mft created for std_validation from input master_desc Array of Files\\n'; for (var i = 0; i < inputs.master_desc.length; i++) { blob += inputs.master_desc[i].path + '\\n'; } return blob; }" ; cwl:entryname "master_desc_mft.mft" ] ] . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , , , , , , , ; cwl:out , , ; cwl:run . sld:default "F" . sld:type xsd:boolean . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-pplacer-path" ] ; sld:default "/usr/local/pplacer/1.1a18" ; sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , ; cwl:out , , , ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "asn2flat" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asn2flat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.match_name)" ] ; sld:type cwl:File . rdfs:label "Assign Naming HMM to Proteins" ; cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . sld:default "nucl" . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:label "Search AntiFam" ; cwl:in , , , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-allow-intersection" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "annotation.mft" ; sld:type xsd:string . sld:type cwl:Directory . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-seq_entries" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:default 60 . sld:type xsd:string , sld:null . sld:default "seq-entries" . sld:type cwl:Directory . rdfs:label "Search Naming HMMs" ; cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-comp_based_stats" ] ; sld:type xsd:string , sld:null . sld:type xsd:int . sld:default true . a cwl:Workflow ; rdfs:comment "univ_wnode" ; rdfs:label "univec_wnode" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-model-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-model-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-model-path" ] ; sld:type cwl:File . cwl:source . sld:default "preliminary-models.asn" . sld:default 1 . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-path" ] ; sld:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin" ; sld:type xsd:string , sld:null . rdfs:label "gpx_qsubmit" ; cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_ids_filename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.instring)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(inputs.instring)" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_reject)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-release_id_list" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-extra-coverage" ] ; sld:type xsd:int , sld:null . cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-cpu" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-cpu" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-cpu" ] ; sld:default 0 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "gilist.mft" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids-manifest" ] ; sld:default "ids.mft" ; sld:type xsd:string , sld:null . sld:default 20 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.stdout_redir)" ] ; sld:type cwl:File . sld:default true . a cwl:CommandLineTool ; rdfs:label "fastaval" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "fastaval.sh" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . sld:type cwl:Directory . sld:default true . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . rdfs:label "Good ab initio annotations" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-x-run" ] ; sld:type xsd:int , sld:null . sld:default 6 . cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hardmask" ] ; sld:type cwl:File , sld:null . sld:default true . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.var_proc_annot_details_xml_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:default "initial_asndisc_diag.xml" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:label "Filter Protein Alignments/align" ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.found_ids_output_file)" ] ; sld:type cwl:File . sld:default 3e-01 . cwl:source , . sld:default false . cwl:source . cwl:source . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-axml" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "orthologous.assembly.gcid" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-z" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-cpu" ] ; sld:default 0 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source , , , , . a cwl:CommandLineTool ; rdfs:label "bact_filter_preserved" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bact_filter_preserved" ) ; cwl:baseCommand ( "bact_filter_preserved" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-masked-locs" ] ; sld:default "masked_locs.asn" ; sld:type xsd:string . sld:default 20 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.seqids_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-s_coverage_threshold" ] ; sld:default 9e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-B" ; cwl:valueFrom "${if (inputs.superkingdom==2) { return true; } else {return false; } }" ] ; sld:default true ; sld:type xsd:boolean . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_impl)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "intermediate.asn" ; sld:type xsd:string , sld:null . sld:default "seq-entry" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:source . sld:default "seq-entry" . cwl:inputBinding [ CommandLineBinding:prefix "-ofull" ] ; sld:default "align_full_cov.asn" ; sld:type xsd:string , sld:null . sld:default "*" . cwl:source . a cwl:CommandLineTool ; rdfs:label "proc_annot_stats" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "proc_annot_stats" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , . cwl:source . cwl:source . rdfs:label "yaml2json" ; cwl:in ; cwl:out ; cwl:run . sld:default "AllSequences" . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-oreject" ] ; sld:default "reject_orfs.asn" ; sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, execution" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-X" "20" "-Q" "-H" "-b" "-q" "-nogenbank" ) ; cwl:baseCommand ( "trnascan_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . sld:default [ a cwl:File ; File:contents "" ; cwl:basename "null" ; cwl:path ] . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:default "seq-entries-b" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.generic_output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.generic_output_name)" ] ; sld:type cwl:File . sld:default 1e-01 . cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File , sld:null . sld:type cwl:Directory . sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default 60 . cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:default "sequences.mft" ; sld:type xsd:string . cwl:source . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ; cwl:valueFrom "${ if( inputs.seq_submit != null ) { return inputs.seq_submit.path; } else { return inputs.entries.path; } }" ] ; sld:default "/dev/null" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outdisc_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-model-path" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-opartial" ] ; sld:default "align_partial_cov.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-master-desc-manifest" ] ; sld:default "master_desc_mft.mft" ; sld:type xsd:string . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . sld:default "mapped-hmm-hits.asn" . cwl:inputBinding [ CommandLineBinding:prefix "-ignore-all-errors" ] ; sld:type xsd:boolean , sld:null . sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "$(inputs.mask)" ] ; sld:default "jobs" ; sld:type xsd:string , sld:null . rdfs:comment "Identify completeness of genome based on core HMM models in CheckM" ; rdfs:label "Run CheckM in PGAP graph" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:default "orf" . rdfs:label "Get Assemblies for Orthologs GenColl ASN" ; cwl:in , ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "Get Proteins" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-inent" ] ; sld:type cwl:File . sld:default "marked-annotation.asn" . sld:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_name)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.f_output)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-hits" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source , . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , . sld:type xsd:boolean . rdfs:comment "The default: setting is for standard call of pgap.cwl (for example, from pgap.py)" ; sld:default "//*[@severity=\"FATAL\"]" ; sld:type xsd:string , sld:null . sld:default true . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-local" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-master-desc" ] ; sld:default "master-desc.asn" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "Extract Assembly Information I" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-level" "top-level" "-nogenbank" ) ; cwl:baseCommand ( "gc_get_molecules" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-X" ] ; sld:type xsd:string , sld:null . rdfs:comment "Sequence ID types that are not allowed." ; cwl:inputBinding [ CommandLineBinding:prefix "-disallow_seqid_type" ] ; sld:type xsd:string , sld:null . sld:default "seq-entry" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:type xsd:int , sld:null . sld:default "dummyarg" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "frequent.seq_ids" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:default "*" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "annot.val.summary" ; sld:type xsd:string . cwl:source . cwl:in , , , , , , , ; cwl:out ; cwl:run . sld:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unplaced" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; cwl:outputBinding [ CommandOutputBinding:glob "cat.out" ] ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:default 12 ; sld:type xsd:int , sld:null . rdfs:label "generate_fscr_feats" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.part_output)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "miniprot" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-S" "-G" "500" "-e" "500" "-p" "0.01" "--outs" "0.01" "--outc" "0.01" "-B" "0" "-L" "15" "-k" "5" "-l" "4" "-n" "2" "-N" "1000" "-t" "16" ) ; cwl:baseCommand ( "miniprot" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:stdout "$(inputs.stdout_redir)" . cwl:source . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "annotation.asn" ; sld:type xsd:string . sld:default "blastdb" . sld:type xsd:boolean . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . rdfs:label "Input blastdb databases" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ; cwl:valueFrom "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . sld:default 50 . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oname)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-filter" ] ; sld:type xsd:string . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-entry-point" ] ; sld:default "empty" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "annot-gb.ent" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-o_orthologs" ] ; sld:default "orthologs.rpt" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . sld:default "F" . cwl:source . rdfs:label "parameter to store the literal 'blast_rules_db'" ; sld:default "blast_rules_db" ; sld:type xsd:string . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.full_output)" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-expansion-ratio" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-expansion-ratio" ] ; sld:type xsd:float . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-blastdb" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "annots.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-best_hit_overhang" ] ; sld:type xsd:float , sld:null . sld:type xsd:int . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "proteins_for_checkm" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-R" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:Directory . cwl:source . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "sequences.asn" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "gp_annot_format" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gp_annot_format" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-order" ] ; sld:type cwl:File , sld:null . rdfs:comment "Allow sequence IDs lacking the gnl| prefix to be interpreted as 'general' db/tag IDs (default is not to allow this)" ; cwl:inputBinding [ CommandLineBinding:prefix "-allow_implicit_gnl" ] ; sld:type xsd:boolean , sld:null . sld:default true . sld:default "add" . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:Directory . sld:default 10000 . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-product-id-prefix" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-product-id-prefix" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-inst-mol" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-inst-mol" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . sld:default "gff3" . sld:default true . sld:default "asn-binary" . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int . rdfs:label "Prepare SPARCLBL input" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , , , , ; cwl:out ; cwl:run . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "result.lst" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-task" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "cmsearch.asn" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-allowable-starts" ] ; sld:default "from-stop-to-stop" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.var_proc_annot_stats_xml_name)" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-submit-block-template" ] ; sld:default "submit_block_template.mft" ; sld:type xsd:string . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . sld:type cwl:File . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var values=[];\n if(inputs.input != null) {\n var lines = inputs.input.contents.split(\"\\n\");\n for(var i=0; i ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . rdfs:comment "XML file with input univec jobs, this parameter is _referential_ which CWL does not like.\n" ; rdfs:label "input_jobs" ; cwl:inputBinding [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Cache Entrez Gene" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "cache_entrez_gene" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:default "asndisc_cpp.applog" ; sld:type xsd:string , sld:null . sld:default "seq-align-set" . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-level" ] ; sld:default "top-level" ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File . cwl:source . sld:default 65 . cwl:inputBinding [ CommandLineBinding:prefix "-annot-request-id" ] ; sld:type xsd:int . sld:default true . cwl:source . sld:type cwl:File . cwl:source . sld:default "blastdir" . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-genus-list" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-genus-list" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-genus-list" ] ; sld:type sld:null ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_accept)" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . cwl:source . sld:default true . cwl:source . sld:default 20 . rdfs:label "gpx_qdump" ; cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "assign_hmm" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "assign_hmm" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; sld:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ; sld:type xsd:string , sld:null . sld:type cwl:File . sld:default 120 . cwl:source . sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "val_stats" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "val_stats" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , . cwl:source . sld:default true . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-min-size" ] ; sld:type xsd:long . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-queries-gc-id-list" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "proteins.xml" ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-hits-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hits-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hits-output" ] ; sld:default "retrieved_hits.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-cutoff" ] ; sld:type xsd:float , sld:null . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . sld:default 5 . cwl:source . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "seq-entry" . cwl:inputBinding [ CommandLineBinding:prefix "-outdir" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "gencoll.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-rfam-amendments" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-rfam-amendments" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-rfam-amendments" ] ; sld:type cwl:File . sld:default "blast.#.asn" . sld:default "predicted-protein" . sld:type xsd:int . sld:default false . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "asn_cleanup" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asn_cleanup" ) ; cwl:baseCommand ( "asn_cleanup" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:default "subject" . cwl:source . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "asn_translator" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asn_translator" ) ; cwl:baseCommand ( "asn_translator" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:default "6000000000" . cwl:source . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-ab_initio-manifest" ] ; sld:default "ab_initio.mft" ; sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . sld:default false . sld:default "score>0 && pct_identity_gapopen_only > 35" . cwl:inputBinding [ CommandLineBinding:prefix "-max-x-ratio" ] ; sld:type xsd:float , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-orfs" ] ; sld:type cwl:File . sld:type xsd:float , sld:null . sld:default 180 . cwl:in , , , , , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:in , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatter ( ) ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-thr" ] ; sld:type cwl:File . rdfs:label "Create Genomic BLASTdb" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:source . a cwl:Workflow ; rdfs:label "Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_fasta_name)" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-rfam-stockholm" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-rfam-stockholm" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-rfam-stockholm" ] ; sld:type cwl:File . sld:default 30 . sld:default true . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_align_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-outformat" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-outformat" ] ; sld:default "text" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-outmetamaster" ] ; sld:default "meta.master.xml" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-oaccept" ] ; sld:default "accept_orfs.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; cwl:outputBinding [ CommandOutputBinding:glob "blastdb.*" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "reduce" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "reduce" ) ; cwl:baseCommand ( "reduce" ) ; cwl:baseCommand ( "reduce" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . sld:default "6000000000" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-tempdir" ] ; sld:default "var" ; sld:type xsd:string . cwl:source . cwl:in , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add_locus_tags" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "add_locus_tags" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs . sld:type cwl:File , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:default true . a cwl:CommandLineTool ; rdfs:label "Filter Full-Coverage Alignments" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "bacterial_protalign_filter" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMax 8000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.uniColl_asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . sld:default 5 . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-accept" ] ; sld:default "accept.asn" ; sld:type xsd:string . sld:default "asn-binary" . sld:default " (align_length >= 50 && pct_identity_gap >= 98) || (align_length >= 100 && pct_identity_gap >= 94) || (align_length >= 200 && pct_identity_gap >= 90)" . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.var_bact_univ_prot_stats_xml_name)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "Extract Assembly Information II" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gc_asm_xml_description" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.names)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.protein_assignments_name)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default "protein database for orhology graph" . cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . rdfs:label "Extract ORF Proteins/proteins" ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "Create Genomic Collection for Bacterial Pipeline, ASN.1 input" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "tt_fscr_calls_pass1" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-contact-as-author-possible" ] ; sld:default true ; sld:type xsd:boolean , sld:null . sld:type xsd:int . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . sld:default "blastp" . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-vdb-path" ] ; sld:type xsd:string , sld:null . rdfs:label "Search All HMMs" ; cwl:in , , , , , , ; cwl:out ; cwl:run . rdfs:comment "The default: setting is for standard call of pgap.cwl (for example, from pgap.py)" ; sld:default "//*[( @severity=\"ERROR\" or @severity=\"REJECT\" )\n and not(contains(@code, \"GENERIC_MissingPubRequirement\")) \n and not(contains(@code, \"SEQ_DESCR_ChromosomeLocation\")) \n and not(contains(@code, \"SEQ_DESCR_MissingLineage\")) \n and not(contains(@code, \"SEQ_DESCR_NoTaxonID\")) \n and not(contains(@code, \"SEQ_DESCR_OrganismIsUndefinedSpecies\"))\n and not(contains(@code, \"SEQ_DESCR_StrainWithEnvironSample\"))\n and not(contains(@code, \"SEQ_DESCR_BacteriaMissingSourceQualifier\"))\n and not(contains(@code, \"SEQ_DESCR_UnwantedCompleteFlag\")) \n and not(contains(@code, \"SEQ_FEAT_BadCharInAuthorLastName\")) \n and not(contains(@code, \"SEQ_FEAT_ShortIntron\")) \n and not(contains(@code, \"SEQ_INST_InternalNsInSeqRaw\")) \n and not(contains(@code, \"SEQ_INST_ProteinsHaveGeneralID\")) \n and not(contains(@code, \"SEQ_PKG_ComponentMissingTitle\")) \n and not(contains(@code, \"SEQ_PKG_NucProtProblem\")) \n]\n" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . sld:default "blastn" . rdfs:label "Assign SPARCL Architecture Names to Proteins" ; cwl:in , , , , ; cwl:out ; cwl:run . rdfs:label "Assign Clusters to Proteins: pre-sort alignments" ; cwl:in , , , , ; cwl:out ; cwl:run . sld:default false . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default "blastdb" ; sld:type xsd:string . cwl:source . rdfs:label "Assign Clusters to Proteins: actual task" ; cwl:in , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "uuid.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "uuid.txt" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , , , ; cwl:out , ; cwl:run . sld:default "subject" . cwl:source . sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . sld:default "seq-entry" . cwl:source . cwl:source , , , . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:default "30 2.2 2.5" . cwl:inputBinding [ CommandLineBinding:prefix "-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-cache" ] ; sld:default "sequence_cache" ; sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-min-pct-ident" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-min-pct-ident" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-val-res-den-xml" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-workers" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-on" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-submission-mode-genbank" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.review_name)" ] ; sld:type cwl:File . sld:type xsd:string . cwl:in , , , , , , ; cwl:out , , ; cwl:run . sld:default "F" . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:default "30 2.2 2.5" . sld:default true . rdfs:label "Get Assemblies for Orthologs GenColl ASN/nucleotide ids" ; cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type xsd:boolean . sld:default "6000000000" . sld:default true . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:default "cleaned-annotation.mft" ; sld:type xsd:string . rdfs:label "Find Struct Protein Hits for Plasmids" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-max-reblast-spans" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "blastp_wnode_struct" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . rdfs:label "Extract ab initio Proteins" ; cwl:in , ; cwl:out , , ; cwl:run . cwl:in , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "bact_univ_prot_stats" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bact_univ_prot_stats" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs , , . sld:default 200 . cwl:inputBinding [ CommandLineBinding:prefix "-XML" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . sld:type xsd:string . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:default true ; sld:type xsd:boolean . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:default true . cwl:source . cwl:source . cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-group" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-group" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ids" ] ; sld:type cwl:File . a cwl:Workflow ; 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:string , sld:null . sld:default 10000 . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "prepare_sparclbl_input" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "prepare_sparclbl_input" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# other_assignments.mft created for prepare_sparclbl_input from input other_assignments Array of Files\\n'; 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:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:default true ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:Directory . cwl:in ; cwl:out , , ; cwl:run [ a cwl:ExpressionTool ; ExpressionTool:expression "${\n var r = {};\n var l = inputs.data.listing;\n var n = l.length;\n for (var i = 0; i < n; i++) {\n if (l[i].basename == 'contam_in_prok_blastdb_dir') {\n r['contam_in_prok_blastdb_dir'] = l[i];\n }\n if (l[i].basename == 'adaptor_fasta.fna') {\n r['adaptor_fasta'] = l[i];\n }\n if (l[i].basename == 'uniColl_path') {\n var ul = l[i].listing;\n var un = ul.length;\n for (var j = 0; j < un; j++) {\n if (ul[j].basename == 'taxonomy.sqlite3') {\n r['taxon_db'] = ul[j];\n }\n }\n }\n }\n return r;\n}\n" ; cwl:inputs ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ] . sld:default "preliminary-models.asn" . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:source . sld:default 1 . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "make_uuid" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "make_uuid" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source . sld:default "score>0 && pct_identity_gapopen_only > 35" . cwl:inputBinding [ CommandLineBinding:prefix "-xml-pgap-details" ] ; sld:default "var_proc_annot_details.xml" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . a cwl:CommandLineTool ; rdfs:label "bact_entries_merge" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "bact_entries_merge" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# ab_initio.mft created for bact_entries_merge from input ab_initio Array of Files\\n';for (var i = 0; i < inputs.ab_initio.length; i++) {blob += inputs.ab_initio[i].path + '\\n';}return blob;}" ; cwl:entryname "ab_initio.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# annotation.mft created for bact_entries_merge from input annotation Array of Files\\n';for (var i = 0; i < inputs.annotation.length; i++) {blob += inputs.annotation[i].path + '\\n';}return blob;}" ; cwl:entryname "annotation.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-blast-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-blast-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-blast-type" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-submit-block" ] ; sld:type cwl:File . sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:default 1000000 . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ; cwl:valueFrom "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)" ] ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-univ-prot-xml" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . sld:default "blast_rules_db" , "blastdb" . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-w" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:default "annot_translated_cds.faa" . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oasn)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . sld:type cwl:Directory . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; 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 "-o" ] ; sld:default "bact_univ_prot_stats_old.xml" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-rfam-amendments" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-tmp" ] ; sld:default "." ; sld:type xsd:string . cwl:in , , , , , ; cwl:out ; cwl:run . sld:default 50000 . sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:default "fasta" ; sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "blast.#.asn" ; sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "genemark_post" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "genemark_post" ) ; cwl:baseCommand ( "genemark_post" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . sld:default "annot-wo-checksum.sqn" . cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-align_filter" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "add_prot_names_to_annot" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "add_prot_names_to_annot" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# proteins.mft created for add_prot_names_to_annot from input proteins Array of Files\\n'; for (var i = 0; i < inputs.proteins.length; i++) { blob += inputs.proteins[i].path + '\\n'; } return blob; }" ; cwl:entryname "proteins.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-hmmsearch-path" ] ; sld:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xslt-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-manifest" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . rdfs:comment "Hidden parameter, hidden within input_jobs:" ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . sld:default "workdir" . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-prot_similarity_threshold" ] ; sld:default 8e-01 ; sld:type xsd:float , sld:null . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:default false ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-chunk-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-chunk-size" ] ; sld:type xsd:long , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "align.asn" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-v" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-p" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:default "delta_sequences.asn" . sld:type cwl:Directory . rdfs:label "Propagate symbols to genes" ; cwl:in , , ; cwl:out ; cwl:run . sld:default 28 . sld:type cwl:File . sld:default "text" . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default 5 . cwl:inputBinding [ CommandLineBinding:prefix "-xml-pgap-output" ] ; sld:default "var_bact_univ_prot_stats.xml" ; sld:type xsd:string . sld:default "sequences.disc.xml" . sld:type xsd:boolean . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-output" ] ; sld:default "annot.val.summary.xml" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "blast.*.asn" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bact_best_evidence_alignments" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-support-threshold" "25.0" "-weak-threshold" "17" ) ; cwl:baseCommand ( "bact_best_evidence_alignments" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# align.mft created for bact_best_evidence_alignments from input align Array of Files\\n'; for (var i = 0; i < inputs.align.length; i++) { blob += inputs.align[i].path + '\\n'; } return blob; }" ; cwl:entryname "align.mft" ] ; cwl:listing [ cwl:entry "${var blob = '# annotation.mft created for bact_best_evidence_alignments from input annotation Array of Files\\n'; for (var i = 0; i < inputs.annotation.length; i++) { blob += inputs.annotation[i].path + '\\n'; } return blob; }" ; cwl:entryname "annotation.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-search" ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:linkMerge "merge_flattened" ; cwl:source , . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "match" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-row" ] ; sld:default 1 ; sld:type xsd:int . sld:default true . sld:type cwl:File . rdfs:label "Extract Protein Targets for Orthology" ; cwl:in , ; cwl:out , , ; cwl:run . 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 "$(inputs.output_file_name)" . cwl:inputBinding [ CommandLineBinding:prefix "-min-chunk-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-min-chunk-size" ] ; sld:type xsd:int , sld:null . sld:default "seq-align-set" . sld:default "blastp.align.asn" . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-best_hit_score_edge" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "checkm-jobs.xml" ; sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; sld:default "JSON" ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "assign_cluster" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "assign_cluster" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.namedb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:default "sequences.mft" ; sld:type xsd:string . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default 1.1e+00 . a cwl:CommandLineTool ; rdfs:label "Run tRNAScan, gather" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unzip" "*" "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "dumb_down_as_required" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "dumb_down_as_required" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , ; cwl:outputs . sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-fast" ] ; sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outval_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default 6 . cwl:inputBinding [ CommandLineBinding:prefix "-min_seq_len" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-softmask" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source , . sld:default "Adaptor" . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-seq-output" ] ; sld:default "entries.asnb" ; sld:type xsd:string , sld:null . rdfs:label "Get Proteins: application run" ; cwl:in , , , , , , ; cwl:out , , ; cwl:run . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-no-external" ] ; sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.onon_match_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.onon_match_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.onon_match_name)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:int . sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-marked-annotation" ] ; sld:default "marked-annotation.asn" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-blastdb" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-max_extent" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "cross_origin_fasta" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cross_origin_fasta" ) ; cwl:baseCommand ( "cross_origin_fasta" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs , . sld:type xsd:int . sld:default "pct_coverage >= 70" . cwl:inputBinding [ CommandLineBinding:prefix "-molinfo" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-molinfo" ] ; sld:type xsd:string , sld:null . sld:default false . cwl:inputBinding [ CommandLineBinding:prefix "-output-annotation" ] ; sld:default "input.asn" ; sld:type xsd:string . sld:default "input_text.asn" . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-xpath-success" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-success" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-success" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xpath-success" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-tmp" ] ; sld:default "." ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Create Assembly From Sequences" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gc_create" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.asn_cache)" ] ] . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "F" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean , sld:null . sld:default 10 . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:label "Map HMM Hits/align" ; sld:type cwl:File . cwl:source . sld:default "GeneMark_hmm_combined.mod" ; sld:type xsd:string . sld:type xsd:float , sld:null . a cwl:Workflow ; rdfs:label "Run genomic CMsearch (Rfam rRNA)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . sld:default "proc_annot_stats.xml" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-annots1" ] ; sld:default "annots1.mft" ; sld:type xsd:string . cwl:source . rdfs:label "Get Prokaryotic Assembly For Orthology" ; cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:source . sld:default "/netmnt/vast01/gp/ThirdParty/GeneMark/" . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "blastn_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "blastn_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ] . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-overlap" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-prots-only" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.nomatch_name)" ] ; sld:type cwl:File . sld:default 4 . cwl:in ; cwl:out ; cwl:run . sld:default 0 . sld:default "1" ; sld:type xsd:string . cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-output-taxid" ] ; sld:default "taxid.txt" ; sld:type xsd:string . sld:type cwl:File . sld:type xsd:string . sld:default 1e+00 . cwl:inputBinding [ CommandLineBinding:prefix "-N" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ignore_all_errors" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-unicoll_sqlite" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:inputBinding [ CommandLineBinding:prefix "-plasmids" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:Directory . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "annot.sqn" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-top-by-score" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_annotation_name)" ] ; sld:type cwl:File . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "" ; rdfs:label "align_find_frequent_sas" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "align_find_frequent" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . sld:default "blast.*.asn" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-style" ] ; sld:type xsd:string . cwl:source . sld:default "contam_in_prok" . cwl:inputBinding [ CommandLineBinding:prefix "-egene-ini" ] ; sld:type cwl:File . cwl:outputSource , ; cwl:pickValue "first_non_null" ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbtype" ] ; sld:type xsd:string . sld:default "c" . rdfs:comment "corresponds to part of default plane in foreign contamination screening graph of classic Gpipe it should go _after_ all screenings, so it goes to a separate degenerate \"plane\" = \"task\" here" ; cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . sld:type cwl:Directory . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:type xsd:string , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asnt" ] ; sld:type cwl:File , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "align.asn" ; sld:type xsd:string . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-prot" ] ; sld:default "prot.mft" ; sld:type xsd:string . cwl:source . sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-blast-hits-sqlite-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-blast-hits-sqlite-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-blast-hits-sqlite-cache" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-blastdbs-manifest" ; cwl:valueFrom "blastdbs.mft" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; 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 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:default "cleaned_input.asn" . sld:default true . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:type xsd:string , sld:null . sld:default "miniprot_slow.paf" ; sld:type xsd:string , sld:null . sld:default 500 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "getfasta" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-skip-duplicates" ) ; cwl:baseCommand ( "getfasta" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# gilist.mft created for getfasta from input gilist Array of Files\\n'; for (var i = 0; i < inputs.gilist.length; i++) { blob += inputs.gilist[i].path + '\\n'; } return blob; }" ; cwl:entryname "gilist.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:default 10 ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dbsize" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:default false ; sld:type xsd:boolean , sld:null . rdfs:label "Input blastdb databases" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-no-compart" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-no-compart" ] ; sld:type xsd:boolean . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "annotation.mft" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:default true . cwl:source . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ; cwl:valueFrom "$(inputs.asn_cache.basename),$(inputs.uniColl_asn_cache.basename)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-alignments" ] ; sld:default "alignments.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "out_asn_name.asn" ; sld:type xsd:string , sld:null . sld:type cwl:File . rdfs:comment "We are not taking here sqn with added annot checksum." ; cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-checkm-path" ] ; sld:default "/root/venv/bin" ; sld:type xsd:string , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-biosource" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-biosource" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:source . cwl:in , , , , , , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.hits_output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.hits_output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.hits_output_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-sequences" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-A-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-A-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-A-manifest" ] ; sld:default "A.mft" ; sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.chomosome_orfs_out)" ] ; sld:type cwl:File . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-top" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "pgapx_input_check" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "pgapx_input_check" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , ; cwl:outputs . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default 1e-01 . a cwl:CommandLineTool ; rdfs:comment "Converts input JSON file to ASN.1 template" ; rdfs:label "pgapx_yaml_ctl" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "pgapx_yaml_ctl" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-gc-assembly" ] ; sld:type cwl:File . cwl:in , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-tab" ] ; sld:type cwl:File , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . rdfs:label "fscr_calls_pass1" ; cwl:in , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-checkm-data-path" ] ; sld:type cwl:Directory . sld:default "true" . cwl:inputBinding [ CommandLineBinding:prefix "-insqn" ] ; sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-logfile" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Get Proteins, bacterial_prot_src" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-no-phage" "-nogenbank" ) ; cwl:baseCommand ( "bacterial_prot_src" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${ var blob = '# blastdbs.mft created for bacterial_prot_src from input \"blastdb\" Array of blastdbs' + '\\n' ; var i = 0; for (i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i] + String.fromCharCode(10); } for (i = 0; i < inputs.all_order_specific_blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.all_order_specific_blastdb[i] + String.fromCharCode(10); } return blob; }" ; cwl:entryname "blastdbs.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.uniColl_asn_cache)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.logfile_output)" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . sld:default "seq-submit" . rdfs:label "Prepare Unannotated Sequences" ; cwl:in , , , , , ; cwl:out , , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "align_sort" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "align_sort" ) ; cwl:baseCommand ( "align_sort" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs . cwl:inputBinding [ CommandLineBinding:prefix "-short-model-limit" ] ; sld:type xsd:int , sld:null . cwl:source . sld:default true . cwl:source . cwl:source , . cwl:source . cwl:source . cwl:source . rdfs:label "Extract ORF Proteins/prot_ids" ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.plasmids_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-selenoproteins" ; cwl:valueFrom "$(inputs.selenoproteins.path)/$(inputs.selenoproteins_db)" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-selenoproteins" ; cwl:valueFrom "$(inputs.selenoproteins.path)/$(inputs.selenoproteins_db)" ] ; sld:type xsd:string . cwl:source . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:comment "Prepare Unannotated Sequences" ; rdfs:label "Prepare Unannotated Sequences" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-submission-mode-genbank" "-nogenbank" ) ; cwl:baseCommand ( "bacterial_prepare_unannotated" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs , , . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type cwl:File , sld:null . sld:type cwl:File . sld:default true . rdfs:label "Get off-frame ORFs/prot_ids" ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "asnvalidate.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:default "output" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "Execute CCF, execution" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" "-ccf-wrapper-path" "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/bin/" "-ccf_conda_env" "/netmnt/vast01/gp/ThirdParty/CRISPRCasFinder/production/ccfenv" "-ccf_root" "/netmnt/vast01/gp/ThirdParty/CRISPRCasFinder/production/CRISPRCasFinder" "-levelMin" "3" "-minNbSpacers" "4" "-mismDRs" "15" "-muscle" "/usr/local/muscle/5.3/bin/muscle" "-ncbi_scripts" "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/current/bin" "-spSim" "10" "-truncDR" "20" "-noMism" ) ; cwl:baseCommand ( "ccf_wnode" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:label "compart_annot2all" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-ofmt" "reference-id" ) ; cwl:baseCommand ( "compart_annot2all" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; cwl:outputBinding [ CommandOutputBinding:outputEval "$(true)" ] ; sld:type xsd:boolean . sld:default true . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-fam" ] ; sld:default "fam.mft" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-blastdb" ; cwl:valueFrom "$(inputs.blastdb_dir.path)/$(inputs.blastdb)" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-pre-annot" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-pre-annot" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-search-proteins" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Get off-frame ORFs" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "get_off_frame_orfs" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , ; cwl:outputs . sld:default true . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-seq-gap" ] ; sld:default 10000 ; sld:type xsd:int , sld:null . cwl:source . sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-found-ids-output" ] ; sld:default "found_ids.txt" ; sld:type xsd:string . sld:type xsd:boolean , sld:null . cwl:source . sld:type cwl:Directory . sld:default 5000 . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . sld:default false . cwl:source . cwl:in , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:prefix "-not-found-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-not-found-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-not-found-output" ] ; sld:default "not_found.ids" ; sld:type xsd:string , sld:null . rdfs:label "univec_wnode" ; cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:string . rdfs:label "Search ab initio for AntiFam" ; cwl:in , , , , , ; cwl:out ; cwl:run . sld:default "yes" . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "annotation.asn" ; sld:type xsd:string . 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:source . sld:type [ sld:items xsd:int ; sld:type sld:array ] . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "proc_annot_stats_or_details.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-onames" ] ; sld:default "names.xml" ; sld:type xsd:string . sld:type cwl:Directory . cwl:source . rdfs:label "Create identification BLASTdb" ; sld:type cwl:Directory . rdfs:label "Get ORFs/outseq" ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.master_desc_name)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "bacterial_orthology_cond" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:NetworkAccess ; NetworkAccess:networkAccess true ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-sure-cutoff" ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.seq_ids_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.seq_ids_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; sld:type xsd:int , sld:null . sld:default "models_training.asn" . sld:type xsd:string , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "input.mft" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:comment "Maximum number of sequence IDs per sequence (0 means unlimited)" ; cwl:inputBinding [ CommandLineBinding:prefix "-max_seqid_count" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "annot.gff" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "application.out" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:default "aligns.mft" ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outdiscxml_name)" ] ; sld:type cwl:File . sld:type xsd:string . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:File . sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ofmt" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xml-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xml-output" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-chromosome_orfs" ] ; sld:default "chromosome_orf.ids" ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-out" ] ; sld:default "reference_protein.seqids" ; sld:type xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type cwl:Directory . cwl:source . sld:default 0e+00 . cwl:inputBinding [ CommandLineBinding:prefix "-long-model-limit" ] ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fasta_name)" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Produce Prokka and Roary ready GFF enhancement = GFF + nuc FASTA" ; rdfs:label "Produce Roary input" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${ return inputs.separator + '\\n'; }" ; cwl:entryname "separator.txt" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.output_name)" . sld:default "-" . cwl:source . sld:default "feats.asn" . cwl:source . cwl:in , , , , , , , , , , , ; cwl:out ; cwl:run ; cwl:when "${var lines = inputs.gc_id_list_orth.contents.split('\\n'); for(var i=0; i cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:in , , , , , ; cwl:run . rdfs:label "Run GeneMark Training (genemark_post)" ; cwl:in , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:in , , , , , , , , ; cwl:out ; cwl:run . sld:type cwl:Directory , 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)" ] ; 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)" ] ; 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)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.in_lds2.basename)" ] ; sld:type cwl:File . rdfs:label "Separate Plasmid ORFs" ; cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-max-unannotated-region" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-it" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:default "yes" . sld:type cwl:Directory . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.not_found_output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.not_found_output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.not_found_output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ifmt" ] ; sld:type xsd:string , sld:null . rdfs:label "Get_off_frame_ORFs task node" ; cwl:in , ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:source . sld:type cwl:Directory . sld:default 30 . sld:default 90 . sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type xsd:string . sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-lds2" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "Run genomic CMsearch" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs . sld:default "megablast" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile)" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "align_sort_ma" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "align_sort" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , ; cwl:outputs . cwl:source . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.selected_blastdb_output)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:default "workdir" . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source , . sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-x" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-manifest" ] ; sld:type cwl:File , sld:null . sld:default true . cwl:source . cwl:in , , , , , , , , ; cwl:out , , , , , ; cwl:run . sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-delta-seqs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-delta-seqs" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-orthologs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-tRNAscan" ] ; sld:default "/netmnt/vast01/gp/ThirdParty/tRNAscan-SE/production/bin/tRNAscan-SE" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-submission-mode-genbank" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-check_min_seqlen" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-filter-accept" ] ; sld:default "pct_coverage = 100 AND qframe = 0 AND sframe = 0 AND cds_internal_stops = 0" ; sld:type xsd:string , sld:null . cwl:in , , , ; cwl:out ; cwl:run . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${ \n var gc = inputs.gencode; \n var gc2 = \"\"; // this is for gc=11\n \n if (gc == 4) { \n gc2 = \"othmito\"; \n } else if (gc == 6) { \n gc2 = \"cilnuc\"; \n } else if (gc == 9) { \n gc2 = \"echdmito\"; \n } else if (gc == 5) { \n gc2 = \"invmito\"; \n } else if (gc == 2) { \n gc2 = \"vertmito\"; \n } else if (gc == 3) { \n gc2 = \"ystmito\"; \n } \n \n return { \n \"output\": gc2 || null \n }; \n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type cwl:File , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_annotation_name)" ] ; sld:type cwl:File . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . sld:default "seq-entry" . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "jobs.xml" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-cmsearch-path" ] ; sld:default "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/third-party/bin" ; sld:type xsd:string , sld:null . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-hmm-path" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxid" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:default 100 . sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "asndisc_cpp" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "asndisc_cpp" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , . cwl:in , , , , ; cwl:out ; cwl:run . sld:default true . cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:default "13G" . sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-trim-low-quality" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-trim-low-quality" ] ; sld:type xsd:boolean , sld:null . cwl:in , ; cwl:out ; cwl:run . rdfs:label "Resolve Annotation Conflicts/annotation" ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File , sld:null . cwl:source . rdfs:label "Find Naming Protein Hits for struct" ; cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:default "protein.fa" ; sld:type xsd:string . sld:type cwl:File . a cwl:Workflow ; rdfs:comment "PGAP pipeline for external usage, powered via containers,\nsimple user input: (FASTA + yaml only, no template)\n" ; rdfs:label "PGAP Pipeline, simple user input, PGAPX-134" ; 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:LoadListingRequirement ; cwl:loadListing "deep_listing" ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-submission-mode-genbank" ] ; sld:type xsd:boolean , sld:null . sld:default "start" . sld:default "best_aligns.asn" . rdfs:label "Good, AntiFam filtered annotations" ; cwl:in , , , ; cwl:out ; cwl:run . sld:default 20 . sld:type cwl:File , sld:null . cwl:source . rdfs:comment "corresponds to part of default plane in foreign contamination screening graph of classic Gpipe it does bunch of generic things so it has to be first" ; rdfs:label "foreign_screening" ; cwl:in , ; cwl:out , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prot_output)" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items xsd:boolean ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ 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; }" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ 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; }" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ var blob = ''; for (var i = 0; i < inputs.blastdb.length; i++) { blob += inputs.blastdb_dir.path + '/' + inputs.blastdb[i]; if(i != inputs.blastdb.length-1) blob += ','; } return blob; }" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-db" ; cwl:valueFrom "${ 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 [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-c-toolkit" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bact_univ_prot_stats_old_xml_name)" ] ; sld:type cwl:File . cwl:source . sld:default 1 . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File . rdfs:label "univec_wnode" ; cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-i" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-conffile" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:comment "This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n proteins:\n default:\n class: File\n path: '/dev/null'\n basename: 'null'\n contents: ''\n" ; rdfs:label "gpx_qsubmit" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ; cwl:entryname "ids.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ; cwl:entryname "ids.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; 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:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# ids.mft created for gpx_qsubmit from input ids Array of Files\\n';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ; cwl:entryname "ids.mft" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.proteins)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "$(inputs.proteins)" ] ; cwl:listing [ cwl:entry "${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 "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; 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)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.blastdb_dir)" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "${ 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 "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }" ] ] . sld:type xsd:string , sld:null . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-B-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-B-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-B-manifest" ] ; sld:default "B.mft" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-annotation" ] ; sld:default "annotation.mft" ; sld:type xsd:string . sld:default 3 . a cwl:CommandLineTool ; rdfs:label "gp_getorf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "gp_getorf" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , ; cwl:outputs . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-xslt-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-xslt-path" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.accept_align_name)" ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:default "annotation.ent" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-order" ] ; sld:default "order.seqids" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.xml_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "cwl split wrapper" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:baseCommand ( "split" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:float . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-d" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:ExpressionTool ; rdfs:label "Split input directory into subpath flows" ; ns1:original_cwlVersion "v1.2" ; ExpressionTool:expression "${\n var r = {};\n var l = inputs.data.listing;\n var n = l.length;\n for (var i = 0; i < n; i++) {\n switch (l[i].basename) {\n case '16S_rRNA':\n r['16s_blastdb_dir'] = l[i];\n break;\n case '23S_rRNA':\n r['23s_blastdb_dir'] = l[i];\n break;\n case 'RF00001.cm':\n r['5s_model_path'] = l[i];\n break;\n case 'SSU.cm':\n r['16s_model_path'] = l[i];\n break;\n case 'LSU.cm':\n r['23s_model_path'] = l[i];\n break;\n case 'AntiFamLib':\n r['AntiFamLib'] = l[i];\n break;\n case 'asn2pas.xsl':\n r['asn2pas_xsl'] = l[i];\n break;\n case 'CDD2':\n r['CDDdata'] = l[i];\n break;\n case 'checkm':\n r['checkm_data_path'] = l[i];\n break;\n case 'cdd_add':\n r['CDDdata2'] = l[i];\n break;\n case 'filter-for-raw-checkm.xml':\n r['filter_for_raw_checkm'] = l[i];\n break;\n case 'gencoll.sqlite':\n r['gc_cache'] = l[i];\n break; \n case 'product_rules.prt':\n r['defline_cleanup_rules'] = l[i];\n break;\n case 'gene_master.ini':\n r['gene_master_ini'] = l[i];\n break;\n case 'packages.versions':\n r['package_versions'] = l[i];\n break;\n case 'rfam-amendments.xml':\n r['rfam_amendments'] = l[i];\n break;\n case 'Rfam.selected1.cm':\n r['rfam_model_path'] = l[i];\n break;\n case 'Rfam.seed':\n r['rfam_stockholm'] = l[i];\n break;\n case 'selenoproteins':\n r['selenoproteins'] = l[i];\n break;\n case 'thresholds.xml':\n r['thresholds'] = l[i];\n break;\n case 'species_genome_size.txt':\n r['species_genome_size'] = l[i];\n break;\n case 'uniColl_path':\n var ul = l[i].listing;\n var un = ul.length;\n for (var j = 0; j < un; j++) {\n switch (ul[j].basename) {\n case 'blast_dir':\n r['identification_db_dir'] = ul[j];\n var wl = ul[j].listing;\n var wn = wl.length;\n for (var h = 0; h < wn; h++) {\n switch (wl[h].basename) {\n case 'order-specific.mft':\n r['all_order_specific_blastdb_file'] = wl[h];\n break;\n }\n }\n break;\n case 'real_hmms':\n r['hmm_path'] = ul[j];\n break;\n case 'real_hmms.tab':\n r['hmms_tab'] = ul[j];\n break;\n case 'naming_hmms':\n r['naming_hmms_combined'] = ul[j];\n break;\n case 'naming_hmms.tab':\n r['naming_hmms_tab'] = ul[j];\n break;\n case 'naming.sqlite':\n r['naming_sqlite'] = ul[j];\n break;\n case 'taxonomy.sqlite3':\n r['taxon_db'] = ul[j];\n break;\n case 'cache':\n r['uniColl_cache'] = ul[j];\n break;\n case 'nuc_cache':\n r['uniColl_nuc_cache'] = ul[j];\n break;\n case 'universal.xml':\n r['univ_prot_xml'] = ul[j];\n break;\n case 'wp-hashes.sqlite':\n r['wp_hashes'] = ul[j];\n break;\n }\n }\n break;\n case 'validation-results.xml':\n r['val_res_den_xml'] = l[i];\n break;\n }\n }\n return r;\n}\n" ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs ; cwl:outputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.order_name )" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-plasmids" ] ; sld:default "plasmids.seqids" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-review" ] ; sld:default "review.asn" ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "checkm" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . sld:default 5 . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File , sld:null . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.calls_name)" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-nogenbank" ] ; sld:type xsd:boolean . cwl:in , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "asn2fasta" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "asn2fasta" ) ; cwl:baseCommand ( "asn2fasta" ) ; cwl:baseCommand ( "asn2fasta" ) ; cwl:baseCommand ( "asn2fasta" ) ; cwl:baseCommand ( "asn2fasta" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , , , ; cwl:outputs , , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory . sld:default 120 . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 4 ; CommandLineBinding:prefix "workflow" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 4 ; CommandLineBinding:prefix "workflow" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "annot_ribo_operons" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "annot_ribo_operons" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , , , , , ; cwl:outputs , , . cwl:inputBinding [ CommandLineBinding:prefix "-gc1" ] ; sld:type cwl:File . sld:default 10 . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-vdb-path" ] ; sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ot" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ot" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oname)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-top" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-top" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "This workflow is specialized for the simple case of XML input that just need a little bit of massaging.\nWe need to have a flavored file because gpx_qsubmit reacts on the presence of a particular form of input instead of relying on a presence of actual non-empty container of objects\n" ; rdfs:label "gpx_qsubmit" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . sld:default "initial_asnval_diag.xml" . sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:label "Execute CRISPR, gather" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-unzip" "*" "-failed-jobs-tolerate-failures" "-produce-empty-file" ) ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion cwl:v1.2 ; cwl:inputs , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.marked_annotation_name)" ] ; sld:type cwl:File . sld:type xsd:string , sld:null .