@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 DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@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/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#jobid>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#merge>
        rdfs:comment      "merge only, the input files are assumed to be pre-sorted" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-m" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-m" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#filterSims>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "sort text file base on given field(s)" ;
        rdfs:label               "GNU sort" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:prefix  "-T" ;
                                     cwl:valueFrom              "$(runtime.tmpdir)"
                                   ]
                                   [ CommandLineBinding:prefix  "-S" ;
                                     cwl:valueFrom              "$(runtime.ram)M"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:prefix  "-T" ;
                                     cwl:valueFrom              "$(runtime.tmpdir)"
                                   ]
                                   [ CommandLineBinding:prefix  "-S" ;
                                     cwl:valueFrom              "$(runtime.ram)M"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "sort" ) ;
        cwl:baseCommand          ( "sort" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#merge> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#key> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#field> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#info> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "sort.error" ;
        cwl:stdout               "sort.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "index_sims_file_md5.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/similarity>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "uncluster_sims.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "index_sims_file_md5.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/key> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/outName> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#outName>
        rdfs:comment      "write result to FILE instead of standard output" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "sort.error" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "sort.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#input>
        rdfs:comment      "Input similarity blast-m8 file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--in_file" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "sort.log" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "sort.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/output> ;
        cwl:valueFrom  "$(self.basename).seq" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sequences>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#input>
        rdfs:comment      "Files to sort" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/clustMap>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#clustMaps> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#bowtieTruncate>
        rdfs:comment      "Return fasta with each sequence truncated to 1024 bps" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--bowtie_truncate" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#simHit>
        rdfs:comment  "Input similarity hit files" ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-i" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/sequences>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/file> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#output>
        rdfs:comment       "Output merged sims and seq file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$([inputs.outName])" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/simHit> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/clustMap> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#featureSeqs>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/key> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/outName> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl>
        a                        cwl:Workflow ;
        rdfs:comment             "create sorted / filtered similarity file with feature sequences, and index by md5" ;
        rdfs:label               "index sim seq" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#filterSims> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#jobid> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#featureSeqs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#clustMaps> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#simSeqOut> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexOut> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).uncluster.sims" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid>
        rdfs:comment      "Sort fasta file by ID" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--sortbyid" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#subsetSeqs>
        rdfs:comment      "Return fasta with each sequence truncated to 1024 bps" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--subset_seqs" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "add_seq2sims.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/simHit>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#filterSims> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#output>
        rdfs:comment       "Concatenated file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/files> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/outName> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sortbyid2tab>
        cwl:default  true .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#sequences>
        rdfs:comment      "Input tabbed sequence file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--seq_file" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/output> ;
        cwl:valueFrom  "$(self[0].basename).sort" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#simSeqOut>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#output>
        rdfs:comment       "The sorted file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/files>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#featureSeqs> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/sequences> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/similarity> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sortbyid2tab> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/sequences> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/output> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/file> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/key>
        cwl:valueFrom  "$([\"2,2\"])" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#clustMap>
        rdfs:comment  "Input cluster mapping files" ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-c" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSeqs/output>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/output> ;
        cwl:valueFrom  "$(self.basename).sort.tab" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#clustMaps>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "expand out similarity file (blast m8) by turning each cluster seed hit into a hit per cluster member\n>uncluster_sims.py <input> <outName> --cfile <cluster> --position <position>\n" ;
        rdfs:label               "uncluster sims" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "--verbose" ]
                                   [ CommandLineBinding:prefix  "--db" ;
                                     cwl:valueFrom              "$(runtime.tmpdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "uncluster_sims.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#position> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#simHit> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#clustMap> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#info> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "uncluster_sims.error" ;
        cwl:stdout               "uncluster_sims.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid2id>
        rdfs:comment      "Transform fasta to ID list, sorted by ID" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--sortbyid2id" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sequences>
        rdfs:comment      "Input sequence file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#position>
        rdfs:comment      "Column position of query in sims file, default is 1" ;
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--position" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "cat.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#files>
        rdfs:comment      "List of files to concatenate" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "uncluster_sims.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#fasta2tab>
        rdfs:comment      "Transform fasta to tabbed" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--fasta2tab" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#outName>
        rdfs:comment      "Output unclustered similarity" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#outName>
        rdfs:comment      "Output index" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--out_file" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#output>
        rdfs:comment       "Output unclustered similarity file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/key>
        cwl:valueFrom  "$([\"1,1\"])" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid2tab>
        rdfs:comment      "Transform fasta to tabbed, sorted by ID" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--sortbyid2tab" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "append feature sequence to each hit line of similarity file\n>add_seq2sims --seq_file --in_sim \n" ;
        rdfs:label               "uncluster sims" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:prefix  "--verbose" ]
                                 ) ;
        cwl:baseCommand          ( "add_seq2sims" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#sequences> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#similarity> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#error> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#info> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "add_seq2sims.error" ;
        cwl:stdout               "add_seq2sims.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self[0]).700.annotation.sims.filter.seq" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#outName>
        rdfs:comment      "Output merged sims and seq" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--out_sim" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#catSeqs/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).feature.seqs" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "add_seq2sims.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/add_seq2sims.tool.cwl#similarity>
        rdfs:comment      "Input similarity file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--in_sim" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#subsetList>
        rdfs:comment      "List of sequences to subset input by, required with subsetSeqs option" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--list" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/output> ;
        cwl:valueFrom  "$(self.basename).index" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexOut>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Concatenate FILE(s) to standard output" ;
        rdfs:label               "GNU cat" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "cat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#files> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "cat.error" ;
        cwl:stdout               "$(inputs.outName)" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#number>
        rdfs:comment      "Number of chunks to load in memory at once before processing, default is 5000" ;
        cwl:default       5000 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--md5_num" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#output>
        rdfs:comment       "Output index file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#fastq2fasta>
        rdfs:comment      "Transform fastq to fasta" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--fastq2fasta" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#output>
        rdfs:comment      "Output sequence file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--output" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "seqUtil.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Utility tool for various sequence file transformations.\n" ;
        rdfs:label               "seqUtil" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "seqUtil" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#fasta2tab> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid2tab> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#subsetList> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#subsetSeqs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sortbyid2id> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#sequences> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#fastq2fasta> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#bowtieTruncate> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#info> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#file> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "seqUtil.error" ;
        cwl:stdout               "seqUtil.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/cat.tool.cwl#outName>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#key>
        rdfs:comment      "start a key at POS1, end it at POS2 (origin 1)" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-k" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-k" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "index m8 format blast file by 2nd column (sorted required)\nreturn: value, seek, length for each record\n>index_sims_file_md5 --in_file <input> --out_file <outName> --md5_num <number>\n" ;
        rdfs:label               "index sims by md5" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "--verbose" ]
                                 ) ;
        cwl:baseCommand          ( "index_sims_file_md5" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#number> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#info> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/index_sims_file_md5.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "index_sims_file_md5.error" ;
        cwl:stdout               "index_sims_file_md5.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sort.tool.cwl#field>
        rdfs:comment      "use SEP instead of non-blank to blank transition, default is tab" ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-t" ;
                            cwl:valueFrom              "$(\"\\u0009\")"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "-t" ;
                            cwl:valueFrom              "$(\"\\u0009\")"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSims/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#unclusterSims/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/seqUtil.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "seqUtil.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#indexSimSeq/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#sortSimSeq/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/index_sim_seq.workflow.cwl#addSeq2Sim/output> .