@prefix LoadListingRequirement: . @prefix NetworkAccess: . @prefix rdf: . @prefix CommandLineBinding: . @prefix xsd: . @prefix Dirent: . @prefix Workflow: . @prefix cwl: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . sld:type cwl:File . cwl:source . cwl:source . cwl:default "megablast" . cwl:default "top-reference-assms" ; cwl:inputBinding [ CommandLineBinding:prefix "-otop-assms" ] ; sld:type xsd:string . cwl:default "minhash" . cwl:source . rdfs:comment "Output is BioTree ASN.1" ; rdfs:label "Build Kmer Tree" ; cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:default "seq-entry" . sld:type xsd:int . a cwl:Workflow ; rdfs:label "assm_assm_blastn_wnode" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs . cwl:default 4e-01 . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:float . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . a cwl:Workflow ; rdfs:label "ani_top_n" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , . cwl:source . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-distances" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-score-method" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-score-method" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "assm_assm_blastn_create_jobs" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-query-assemblies-manifest" "q.mft" "-target-assemblies-manifest" "t.mft" ) ; cwl:baseCommand ( "assm_assm_blastn_create_jobs" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${\n var blob = '# q.mft created for assm_assm_blastn_create_jobs from input \"queries_gc_id_list\" File\\n'; \n if(inputs.queries_gc_id_list != null) { blob += inputs.queries_gc_id_list.path + '\\n'; } \n return blob; \n}" ; cwl:entryname "q.mft" ] ; cwl:listing [ cwl:entry "${\n var blob = '# t.mft created for assm_assm_blastn_create_jobs from input \"subjects_gc_id_list\" File\\n'; \n if(inputs.subjects_gc_id_list != null) { blob += inputs.subjects_gc_id_list.path + '\\n'; } \n return blob; \n}" ; cwl:entryname "t.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-ref-assembly-taxid" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-asn-cache" ] ; sld:type cwl:Directory , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-gcextract2-sqlite" ] ; sld:type cwl:File . sld:type cwl:File . cwl:default "combined_kmer_cache.sqlite" ; cwl:inputBinding [ CommandLineBinding:prefix "-output-kmer-sqlite-file" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-obin" ] ; sld:type xsd:string , sld:null . sld:type xsd:boolean . sld:type xsd:boolean . cwl:default 25 . sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_jobs)" ] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-kmer-cache-uri" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-kmer-cache-uri" ] ; sld:type cwl:File . cwl:default "minhash" . cwl:default "output.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-soft_masking" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type cwl:File . sld:type xsd:string , sld:null . cwl:default true . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:default 100 . cwl:source . rdfs:comment "this parameter is fixed for this command line workflow, because the output is defined as single file\n" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-num-partitions" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "-kmer-cache-uri" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.otop_assms_xml)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "distances.##.gz" . cwl:source . a cwl:CommandLineTool ; rdfs:label "kmer_top_identification" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "kmer_top_identification" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-kmer-output-dir" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-input-kmer-sqlite-uri" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default "sqlite-listing.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-listing" ] ; sld:type xsd:string . cwl:source . rdfs:comment "compares kmers from different genomes in the input and produces distance matrix\nfilled only for ref vs current elements\n" ; rdfs:label "Compare Kmer" ; cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "xsltproc" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "xsltproc" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "output" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string , sld:null . rdfs:comment "This is rather standard blast" ; rdfs:label "Assembly Assembly BLASTn" ; cwl:in , , , , , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . rdfs:comment "Produces the list of all keys in sqlite database" ; rdfs:label "List SQLITE kmer cache contents" ; cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-batch-size" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "kmer_build_tree" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "kmer_build_tree" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:comment "Pairwise comparison" ; rdfs:label "tt_kmer_compare_wnode" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs . a cwl:CommandLineTool ; rdfs:label "kmer_extract_wnode" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "kmer_extract_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.input)" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-max_target_seqs" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "submit_kmer_compare" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "submit_kmer_compare" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${return '# submit_kmer_compare.kmer-files.mft created for submit_kmer_compare from input kmer_list File\\n' + inputs.kmer_list.path + '\\n'; }" ; cwl:entryname "submit_kmer_compare.kmer-files.mft" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , , ; cwl:out , ; cwl:run . cwl:in , , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-file-uri" ] ; sld:type cwl:Directory . cwl:source . rdfs:comment "This new step will combine together reference kmer store and newly created kmer store for a new assembly\n" ; rdfs:label "Combine kmer SQLITE" ; cwl:in , ; cwl:out ; cwl:run . cwl:default true . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-ref-assembly-id" ] ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:default "expected_kmer_files" . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-evalue" ] ; sld:type xsd:float , sld:null . cwl:default "true" . cwl:inputBinding [ CommandLineBinding:prefix "-no-merge" ] ; sld:type xsd:boolean . rdfs:comment "computes kmers for input genome (Extract_Kmers_From_Input___entry)\nproduces kmer files (.gz and xml)\nit will have a new output: out_kmer_dir\n" ; rdfs:label "Extract Kmers From Input" ; cwl:in , , ; cwl:out ; cwl:run . cwl:default "distances.*.gz" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default "ani-tax-report.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "This workflow is specialized for the case when there is an XML input \n" ; rdfs:label "gpx_qsubmit" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gpx_qsubmit" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ 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:inputBinding [ CommandLineBinding:prefix "-word_size" ] ; sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "kmer_top_n_extract" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , . cwl:inputBinding [ CommandLineBinding:prefix "-ANI_cutoff" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-workers-per-cpu" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:default "submit_kmer_compare.ref-kmer-files.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-ref-kmer-files-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-ref-kmer-files-manifest" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-ref-assembly-id" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:default "dont-unzip" . cwl:source . cwl:default "*" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gc_extract_ids" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gc_extract_ids" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs . cwl:default "target_and_matches.ids" . sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:in , , , , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-threshold" ] ; sld:type xsd:float , sld:null . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-ref-assembly-taxid" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:default "output.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:default true . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-mode" ] ; sld:type xsd:string , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:default "boolean" . a cwl:CommandLineTool ; rdfs:label "assm_assm_blastn_wnode" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "assm_assm_blastn_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${\n var blob = '# queries-and-targets.mft created for assm_assm_blastn_wnode from input \"target_set\" File\\n'; \n if(inputs.target_set != null) { \n for(var i=0; i cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . sld:type xsd:string , sld:null . sld:type cwl:File . sld:type cwl:File . rdfs:comment "Identifies Top N hits to input genome by kmer distances \nproduces distances XML and list of matching genomes (storage URIs)\n" ; rdfs:label "Identify Top N hits by Kmer" ; cwl:in , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-NxM-threshold" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.kmer_output_dir)" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:prefix "-min-gap" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-gapopen" ] ; sld:type xsd:int , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o)" ] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:default "annot.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o-annot" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-xml-jobs" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-gc-id-list" ] ; sld:type cwl:File , sld:null . cwl:default "tree_bin.asn" . a cwl:CommandLineTool ; rdfs:label "gc_get_assembly" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gc_get_assembly" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-tax-syn-table" ] ; sld:type cwl:File . cwl:default "subject" ; cwl:inputBinding [ CommandLineBinding:prefix "-affinity" ] ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:source . sld:type cwl:Directory . cwl:default "gencoll.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:default "boolean" . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-subseq-size" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . sld:type xsd:int . rdfs:comment "This new step will convert input .kmer.gz (kmer_file) and .xml (kmer_metadata_file)\ninto new sqlite database\nThe program we are calling here takes a directory input\n" ; rdfs:label "Convert Kmer files to SQLITE" ; cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-dist-method" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-dist-method" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-gapextend" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_kmer_file)" ] ; sld:type cwl:File . rdfs:comment "transform ANI taxcheck report XML file to Genbank suitable (SMART equivalent) text report" ; cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-kmer-cache-uri" ] ; sld:type cwl:File . cwl:source . cwl:default 28 . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-input-jobs" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:comment "We need $(inputs.seq_entry) to be a local file to the current subdirectory since the file name goes to output.xml, a notorious file with files.\n" ; rdfs:label "submit_kmer_extract" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "submit_kmer_extract" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.seq_entry)" ] ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:default "gencoll.asn" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:default "tree_text.asn" . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-bases-per-call" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-fast" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-type" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "concatenates input File[] to output File" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:stdout "$(inputs.output_file_name)" . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "kmer_top_n_extract" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "kmer_top_n_extract" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs , . cwl:source . cwl:default "distances.##.gz" . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.otext)" ] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-distances" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.oxml)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:prefix "-asn-cache" ] ; sld:type sld:null ; sld:type [ sld:items cwl:Directory ; sld:type sld:array ] . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string . cwl:source . cwl:default 10000 . cwl:default "dont-unzip" . cwl:default "concatenated.file" ; sld:type xsd:string . cwl:default "subject" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-use-common-components" ] ; sld:type xsd:boolean . cwl:default "local_kmer_cache.sqlite" ; cwl:inputBinding [ CommandLineBinding:prefix "-db-uri" ] ; sld:type xsd:string . sld:type xsd:float , sld:null . rdfs:comment "we hope to use this to pass instead of file list" ; cwl:outputSource ; sld:type cwl:Directory . cwl:default "leaf-count-ascending" . cwl:inputBinding [ CommandLineBinding:prefix "-window_size" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-overlap" ] ; sld:type xsd:int , sld:null . cwl:default 1 . a cwl:CommandLineTool ; rdfs:label "gpx_make_outputs" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "gpx_make_outputs" ) ; cwl:baseCommand ( "gpx_make_outputs" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs . a cwl:Workflow ; rdfs:label "bacterial_kmer" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "-ref-assemblies" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "gcaccess_from_list" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs . cwl:default "matches.txt" ; cwl:inputBinding [ CommandLineBinding:prefix "-omatches" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "ani_top_identification" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-nogenbank" ) ; cwl:baseCommand ( "ani_top_identification" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , ; cwl:outputs , . cwl:inputBinding [ CommandLineBinding:prefix "-gcextract2-sqlite" ] ; sld:type cwl:File . cwl:default 500000000 . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o_annot)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-skip-markup" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "-N" ] ; sld:type xsd:int , sld:null . cwl:default "var_proc_annot_stats.val.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; sld:type xsd:string . cwl:default "top_distances.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-oxml" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . sld:type cwl:File . sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "submit_kmer_compare" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "submit_kmer_compare" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# submit_kmer_compare.ref-kmer-files.mft created for submit_kmer_compare from input ref_kmer_list File\\n'; if ( inputs.ref_kmer_list == null) { return blob; } else { return blob + inputs.ref_kmer_list.path + '\\n'; }}" ; cwl:entryname "submit_kmer_compare.ref-kmer-files.mft" ] ; cwl:listing [ cwl:entry "${return '# submit_kmer_compare.kmer-files.mft created for submit_kmer_compare from input kmer_list File\\n' + inputs.kmer_list.path + '\\n'; }" ; cwl:entryname "submit_kmer_compare.kmer-files.mft" ] ] . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file)" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.O)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.O)" ] ; sld:type cwl:Directory . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-compart" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:default 1 . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_xml_file_name)" ] ; sld:type cwl:File . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-output" ] ; sld:type xsd:string . cwl:source . cwl:default "kmer_dir" ; sld:type xsd:string . sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:Directory . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_dir)" ] ; sld:type cwl:Directory . sld:type xsd:float , sld:null . sld:type cwl:File . rdfs:comment "identify top N ANI" ; rdfs:label "Identify Top N ANI" ; cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-sort" ] ; sld:type xsd:string , sld:null . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "-max-jobs" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:int . cwl:default "kmer-tax-report.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-otop-assms-xml" ] ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-min-region" ] ; sld:type xsd:int , sld:null . rdfs:comment "Input is list of reference assemblies, not to be mixed with list of URIs" ; rdfs:label "Get Top Assemblies GenColl ASN" ; cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:comment "Produces the list of all keys in sqlite database" ; rdfs:label "list_kmer_sqlite.cwl" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "list_kmer_sqlite" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs . cwl:default "queries-and-targets.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-target-set-manifest" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-taxon-db" ] ; sld:type cwl:File . cwl:source . cwl:default true . cwl:inputBinding [ CommandLineBinding:prefix "-query-assembly" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:Directory . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "*" ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . sld:type cwl:File . sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-max-batch-length" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-N" ] ; sld:type xsd:int , sld:null . sld:type cwl:File . a cwl:Workflow ; rdfs:label "kmer_seq_entry_extract_wnode" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:default 1e-04 . cwl:in , , ; cwl:out ; cwl:run . cwl:default 20 . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:default 1 . cwl:inputBinding [ CommandLineBinding:prefix "-merge-engine" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . rdfs:comment "Takes XML file with top distances between matches and reference assembly taxid\nproduces XML tax report and list of top matched assemblies \n" ; rdfs:label "Extract Top Assemblies" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-seq-entry" ] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-input" ] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "kmer_build_tree" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs . cwl:source . sld:type cwl:Directory . sld:type cwl:File . cwl:default "ani-tax-report.txt" . sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-gc-cache" ] ; sld:type cwl:File . cwl:default 1e-01 . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . sld:type cwl:File . sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "kmer_compare_wnode" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "kmer_compare_wnode" ) ; cwl:baseCommand ( "kmer_compare_wnode" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# submit_kmer_compare.ref-kmer-files.mft created for kmer_compare_wnode from input ref_kmer_list File\\n'; if(inputs.ref_kmer_list == null ) { return blob; } else { return blob + inputs.ref_kmer_list.path + '\\n'; } }" ; cwl:entryname "submit_kmer_compare.ref-kmer-files.mft" ] ; cwl:listing [ cwl:entry "$(inputs.kmer_list.path)" ; cwl:entryname "submit_kmer_compare.kmer-files.mft" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "${var blob = '# submit_kmer_compare.ref-kmer-files.mft created for kmer_compare_wnode from input ref_kmer_list File\\n'; if(inputs.ref_kmer_list == null ) { return blob; } else { return blob + inputs.ref_kmer_list.path + '\\n'; } }" ; cwl:entryname "submit_kmer_compare.ref-kmer-files.mft" ] ; cwl:listing [ cwl:entry "$(inputs.kmer_list.path)" ; cwl:entryname "submit_kmer_compare.kmer-files.mft" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "-gc-cache" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-otext" ] ; sld:type xsd:string , sld:null . cwl:default "AllSequences" . sld:type xsd:int , sld:null . rdfs:comment "Input is input ASN.1 file for our target assembly" ; rdfs:label "Extract Input GenColl IDs" ; cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:default 2 . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_glob)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_glob)" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-minhash-signature" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-minhash-signature" ] ; sld:type xsd:string , sld:null . sld:type xsd:int . a cwl:Workflow ; rdfs:label "kmer_ref_compare_wnode" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-merge-align-filter" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:Directory . a cwl:CommandLineTool ; rdfs:comment "Combine together reference kmer store and newly created kmer store for a new assembly" ; rdfs:label "combine_kmer_sqlite.cwl" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "combine_kmer_sqlite" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-input-path" ] ; sld:type cwl:Directory . rdfs:comment "compares kmers from top hits to query genome in the input and produces distance matrix for subsequent tree: all-against-all. This is the most downstream node requiring sqlite cache\n" ; rdfs:label "Compare Kmer pairwise" ; cwl:in , , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-affinity-bin" ] ; sld:type xsd:int , sld:null . cwl:default 10 . cwl:default true . cwl:default "minhash" . sld:type cwl:File , sld:null . cwl:default "submit_kmer_compare.kmer-files.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-kmer-files-manifest" ] ; sld:type xsd:string . cwl:default 8e-01 . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.omatches)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Convert input .kmer.gz (kmer_file) and .xml (kmer_metadata_file)\ninto new sqlite database\nTakes a directory input\n" ; rdfs:label "kmer_files2sqlite.cwl" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "kmer_files2sqlite" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ Dirent:writable false ; cwl:entry "${ var blob = ''; for (var i = 0; i < inputs.kmer_dir.listing.length; i++) { var nameext = inputs.kmer_dir.listing[i].nameext; if ( nameext == \".gz\" ) { blob += inputs.kmer_dir.listing[i].path + '\\n'; } } return blob; }" ; cwl:entryname "keys.ids" ] ; cwl:listing [ Dirent:writable false ; cwl:entry "$(inputs.kmer_dir)" ] ] . sld:type xsd:int . cwl:default "keys.ids" ; cwl:inputBinding [ CommandLineBinding:prefix "-gencoll-ids" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "gpx_qdump" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "gpx_qdump" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs . cwl:default "expected_kmer_files" ; cwl:inputBinding [ CommandLineBinding:prefix "-expected-output" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-release_id_list" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:default "submit_kmer_compare.kmer-files.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-kmer-files-manifest" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-kmer-files-manifest" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-task" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type cwl:File , sld:null . cwl:default "distances.*.gz" . cwl:default "outdir" ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-O" ] ; sld:type xsd:string . cwl:default 250 . cwl:default "submit_kmer_compare.kmer-files.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-kmer-files-manifest" ] ; sld:type xsd:string . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "-backlog" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.out_name)" ] ; sld:type cwl:File . rdfs:label "Glue SQLITE keys" ; cwl:in , ; cwl:out ; cwl:run . cwl:default "tree-merger" . sld:type xsd:string , sld:null . cwl:default "((reciprocity = 3 AND align_length_ungap >= 5) OR align_length > 1000) AND pct_identity_gap > 25" . rdfs:comment "Used only to be preserved" ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:default "minhash" . cwl:source . cwl:default 18 ; cwl:inputBinding [ CommandLineBinding:prefix "-k" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-unzip" ] ; sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.o)" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.otop_assms)" ] ; sld:type cwl:File . cwl:source . cwl:default "jobs.xml" ; cwl:inputBinding [ CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:default "submit_kmer_compare.ref-kmer-files.mft" ; cwl:inputBinding [ CommandLineBinding:prefix "-ref-kmer-files-manifest" ] ; sld:type xsd:string . cwl:default 150 .