@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix Dirent: .
@prefix cwl: .
@prefix File: .
cwl:source .
cwl:default false .
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string , sld:null .
sld:type cwl:Directory .
cwl:default "align.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-o" ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"-excluded-seqs" ] ;
sld:type cwl:File , sld:null .
cwl:source .
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.onon_match_name)" ] ;
sld:type cwl:File .
cwl:default "blastn" .
cwl:inputBinding [ CommandLineBinding:prefix
"-batch-size" ] ;
sld:type xsd:int , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:default "feats.asn" .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-asn-cache" ] ;
sld:type cwl:Directory , sld:null .
cwl:linkMerge "merge_flattened" ;
cwl:source .
cwl:default 1 .
a cwl:CommandLineTool ;
rdfs:comment "This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n proteins:\n default:\n class: File\n path: '/dev/null'\n basename: 'null'\n contents: ''\n" ;
rdfs:label "gpx_qsubmit" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "gpx_qsubmit" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "${var blob = '# 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 "${ var cs=0; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ var cs=1; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ var cs=0; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.proteins)"
]
] .
cwl:inputBinding [ CommandLineBinding:prefix
"-queries-gc-id-list" ] ;
sld:type cwl:File , sld:null .
cwl:default 1e-01 .
cwl:source .
cwl:default "frequent.seq_ids" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-out" ] ;
sld:type xsd:string .
cwl:inputBinding [ CommandLineBinding:prefix
"-best_hit_overhang" ] ;
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-subseq-size" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:string , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-NxM-threshold" ] ;
sld:type xsd:int , sld:null .
cwl:source .
rdfs:label "align_filter" ;
cwl:in , , , , , ;
cwl:out , ;
cwl:run .
sld:type xsd:string , sld:null .
sld:type xsd:string , sld:null .
sld:type xsd:float , sld:null .
cwl:default "seq-align-set" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-ifmt" ] ;
sld:type xsd:string .
cwl:source .
cwl:default true ;
cwl:inputBinding [ CommandLineBinding:prefix
"-soft_masking" ] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:inputBinding [ CommandLineBinding:prefix
"-source" ] ;
sld:type xsd:string .
cwl:default "yes" .
sld:type xsd:boolean , sld:null .
cwl:in , , , , , , , ;
cwl:out ;
cwl:run .
sld:type xsd:string , sld:null .
cwl:default 90 .
cwl:source .
cwl:default [ a cwl:File ;
File:contents "" ;
cwl:basename "null" ;
cwl:path
] .
cwl:default "vector" .
cwl:default "contam_in_prok" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.o_name)" ] ;
sld:type cwl:File .
cwl:default "megablast" .
cwl:default "seq-align-set" .
cwl:default "*" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-unzip" ] ;
sld:type xsd:string , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-jobs" ] ;
sld:type cwl:File .
cwl:source .
cwl:source .
sld:type xsd:string , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_glob)" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-max-batch-length" ] ;
sld:type xsd:int , sld:null .
sld:type xsd:string .
cwl:source .
cwl:default "jobs.xml" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-o" ] ;
sld:type xsd:string .
cwl:default 250 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-max_target_seqs" ] ;
sld:type xsd:int , sld:null .
cwl:linkMerge "merge_flattened" ;
cwl:source .
a cwl:CommandLineTool ;
rdfs:label "align_filter" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "align_filter" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "${var blob = '# 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:default "aligns.mft" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-input-manifest" ] ;
sld:type xsd:string , sld:null .
cwl:source .
sld:type xsd:float , sld:null .
a cwl:CommandLineTool ;
rdfs:label "gpx_make_outputs" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "gpx_make_outputs" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs .
a cwl:Workflow ;
rdfs:label "tt_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:requirements [ a cwl:MultipleInputFeatureRequirement ] .
a cwl:CommandLineTool ;
rdfs:label "generate_fscr_feats" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "generate_fscr_feats" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs .
rdfs:label "generate_fscr_feats" ;
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"-o" ] ;
sld:type xsd:string .
cwl:default 1e-04 .
cwl:default true .
cwl:source .
cwl:source .
cwl:default " (align_length >= 50 && pct_identity_gap >= 98) || (align_length >= 100 && pct_identity_gap >= 94) || (align_length >= 200 && pct_identity_gap >= 90)" .
cwl:default 1e-02 ;
cwl:inputBinding [ CommandLineBinding:prefix
"-evalue" ] ;
sld:type xsd:float , sld:null .
cwl:in , , , , , , , , , , ;
cwl:out ;
cwl:run .
cwl:inputBinding [ CommandLineBinding:prefix
"-input" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix "-blastdb" ;
cwl:valueFrom "$(inputs.blastdb_dir.path)/$(inputs.blastdb)"
] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-input" ] ;
sld:type cwl:File .
sld:type xsd:int , sld:null .
cwl:default "true" .
sld:type cwl:Directory , sld:null .
cwl:linkMerge "merge_flattened" ;
cwl:source .
sld:type cwl:File .
cwl:linkMerge "merge_flattened" ;
cwl:source .
cwl:default "output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type xsd:string , sld:null .
cwl:outputSource ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-dust" ] ;
sld:type xsd:string , sld:null .
a cwl:CommandLineTool ;
rdfs:label "blastn_wnode" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "blastn_wnode" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , ,