@prefix LoadListingRequirement: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix Dirent: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
a cwl:Workflow ;
rdfs:label "Bacterial Annotation, pass 2, blastp-based functional annotation (first pass)" ;
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 ] ;
cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] .
cwl:source .
cwl:source .
rdfs:label "goes to protein_alignment/Seed Search Compartments/compartments" ;
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:default "result.lst" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-output" ] ;
sld:type xsd:string .
cwl:default "output" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-O" ] ;
sld:type xsd:string , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-nogenbank" ] ;
sld:type xsd:boolean , sld:null .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-no-merge" ] ;
sld:type xsd:boolean , sld:null .
sld:type cwl:File , sld:null .
sld:type xsd:string .
cwl:source .
sld:type xsd:string .
cwl:source .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-max_target_seqs" ] ;
sld:type xsd:int , sld:null .
cwl:source .
cwl:default "subject" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-affinity" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:label "Map HMM Hits" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "bacterial_hit_mapping" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , ;
cwl:outputs .
cwl:default "mapped-hmm-hits.asn" ;
cwl:inputBinding [ CommandLineBinding:prefix
"-o" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:int .
cwl:inputBinding [ CommandLineBinding:prefix
"-threshold" ] ;
sld:type xsd:int , sld:null .
cwl:default "no" .
cwl:source .
cwl:source .
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-unzip" ] ;
sld:type xsd:string , sld:null .
cwl:default "subject" .
sld:type xsd:string .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "This workflow is specialized for the case when there is an LDS2 input LDS2 is a _reference_ object, the kind that CWL does not like we need to provide actual input: proteins which matches the name of ASN.1 object references in LDS2 Another limitation is that it can handle no more than two item arrays in blastdb_dir and asn_cache Workaround used so far: in:\n proteins:\n default:\n class: File\n path: '/dev/null'\n basename: 'null'\n contents: ''\n" ;
rdfs:label "gpx_qsubmit" ;
ns1:original_cwlVersion "v1.0" ;
cwl:baseCommand ( "gpx_qsubmit" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , , , , , , , , , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "${var blob = '';for (var i = 0; i < inputs.ids.length; i++) {blob += inputs.ids[i].path + '\\n';}return blob;}" ;
cwl:entryname "ids.mft"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ var cs=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 "${ var cs=0; var s=inputs.blastdb_dir.length-1; var as = cs; if(as >= s) {as = s }; return inputs.blastdb_dir[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "$(inputs.proteins)"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ var cs=1; var s=inputs.asn_cache.length-1; var as = cs; if(as >= s) {as = s }; return inputs.asn_cache[as]; }"
] ;
cwl:listing [ Dirent:writable false ;
cwl:entry "${ 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:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-input-jobs" ] ;
sld:type cwl:File .
cwl:inputBinding [ CommandLineBinding:prefix
"-ofmt" ] ;
sld:type xsd:string , sld:null .
sld:type xsd:boolean .
cwl:default false .
rdfs:label "Remove off-frame ORFs" ;
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source .
cwl:source .
cwl:default false .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.mask)?*$(inputs.suffix)" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type xsd:string .
rdfs:label "Create identification BLASTdb" ;
sld:type cwl:Directory .
cwl:in , , , , , , , , , , , , , , , , , , , , ;
cwl:out ;
cwl:run ;
cwl:scatter ( ) .
cwl:inputBinding [ CommandLineBinding:prefix
"-word_size" ] ;
sld:type xsd:int .
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
"-operation" ] ;
sld:type xsd:string .
sld:type xsd:string .
cwl:default 1e+00 .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_xml_jobs)" ] ;
sld:type cwl:File .
rdfs:label "Extract ORF Proteins/proteins" ;
sld:type cwl:File .
sld:type xsd:int .
sld:type xsd:string .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
4 ] ;
sld:type cwl:File .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-subjects-gc-id-list" ] ;
sld:type cwl:File , sld:null .
sld:type xsd:boolean .
cwl:default "seq-align-set" .
cwl:source .
rdfs:label "Find Naming Protein Hits I" ;
cwl:in , , , , , , , , , , , , , , , , , , , , , , , , ;
cwl:out ;
cwl:run .
sld:type xsd:boolean .
cwl:inputBinding [ CommandLineBinding:prefix
"-queries-gc-id-list" ] ;
sld:type cwl:File , sld:null .
cwl:source , .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_dir)" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
cwl:source .
cwl:source .
sld:type xsd:int .
sld:type xsd:float , sld:null .
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:prefix "-asn-cache"
] ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
sld:type xsd:boolean .
cwl:source .
cwl:inputBinding [ CommandLineBinding:prefix
"-batch-size" ] ;
sld:type xsd:int , sld:null .
cwl:default false .
a cwl:Workflow ;
rdfs:label "blastp_wnode_naming" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , , , ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , , , , , , , , , , , ,