@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl>
        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               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#output_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#input_path> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#annots> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/input_jobs> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#annots>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump/annots> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#jobs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#output>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#input_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#annots>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#go>
        sld:type  [ sld:items  xsd:boolean ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/outdir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#asn_cache> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#input_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input-jobs" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/asn_cache> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/seqids> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#outdir>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_dir)" ] ;
        sld:type           cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Execute CRISPR" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#go> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#annots> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-O" ] ;
        sld:default       "output" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl#output_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output" ] ;
        sld:default       "ncbi_crispr.out" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl>
        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               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/ccf_wnode.cwl#outdir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_submit/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#seqids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#asn_cache>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#seqids>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#asn_cache>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-asn-cache" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl>
        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               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#output> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#asn_cache> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qsubmit.cwl#seqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-ids" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump/input_path> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_dump/annots> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#Execute_CRISPR_wnode/asn_cache>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl#asn_cache> .