@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/Tools/find_contig_lca.tool.cwl#info>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "find_contig_lca.log" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/profileType>
        cwl:valueFrom  "lca" .

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

<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/abundance-clca.workflow.cwl#sourceStats/coverage>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#coverage> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#rnaLCA>
        rdfs:comment      "Input expanded rna LCA file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--rna" ] ;
        sld:type          cwl:File .

<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  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        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: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/Workflows/abundance-clca.workflow.cwl#md5Profile/coverage>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#coverage> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/cluster>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protClustMap> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).700.annotation.source.stats" .

<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/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/uncluster_sims.tool.cwl#error>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "uncluster_sims.error" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "uncluster_sims.error" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/protLCA>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortProt/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/clustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/simHit> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/position> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/outName> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/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/contig-lca.workflow.cwl#unclusterRna/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaExpandLca> ;
        cwl:valueFrom  "$(self.basename).uncluster" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/simHit>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaExpandLca> ;
        cwl:valueFrom  "${ return [self]; }" .

<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/Tools/sims_abundance.tool.cwl#outName>
        rdfs:comment      "Output abundance profile" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/key> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/input> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/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#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/abundance-clca.workflow.cwl#md5Profile/md5index>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5index> .

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

<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
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-i" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/clustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/position> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/simHit> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/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/contig-lca.workflow.cwl#m5nrSCG>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl>
        a                        cwl:Workflow ;
        rdfs:comment             "abundace profiles from annotated files, for protein and/or rna" ;
        rdfs:label               "abundance" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile> ;
        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/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#expandSims> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#filterSims> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5index> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#jobid> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#m5nrSCG> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#coverage> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5ProfileOut> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfileOut> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStatsOut> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/scgs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/rnaLCA> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/protLCA> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaClustMap>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/simHit>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protExpandLca> ;
        cwl:valueFrom  "${ return [self]; }" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl>
        a                        cwl:Workflow ;
        rdfs:comment             "create LCA consistant across input contigs contigs\norder of precedence - rRNA, single copy gene, LCA of genes\n" ;
        rdfs:label               "contig LCA" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortProt> ;
        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/contig-lca.workflow.cwl#rnaExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#jobid> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#coverage> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#m5nrSCG> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaClustMap> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#contigLCA> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/cluster>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protClustMap> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#jobid>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfileOut>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/contigLCA> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/input>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/output> ;
        cwl:valueFrom  "${ return [self]; }" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).700.annotation.md5.abundance" .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortProt/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/output> ;
        cwl:valueFrom  "$(self[0].basename).sort" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/rnaLCA>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/output> .

<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/Tools/sims_abundance.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "create abundance profile from expanded annotated sims files\nmd5:    sims_abundance.py -t md5 -i <input> -o <output> --coverage <coverage> --cluster <cluster> --md5index <md5index>\nlca:    sims_abundance.py -t lca -i <input> -o <output> --coverage <coverage> --cluster <cluster>\nsource: sims_abundance.py -t source -i <input> -o <output> --coverage <coverage> --cluster <cluster>\n" ;
        rdfs:label               "abundance profile" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "sims_abundance.py" ) ;
        cwl:baseCommand          ( "sims_abundance.py" ) ;
        cwl:baseCommand          ( "sims_abundance.py" ) ;
        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                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgrast/pipeline:4.03"
                                 ] ;
        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  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/LoadListingRequirement> ] ;
        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/sims_abundance.tool.cwl#profileType> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#md5index> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#coverage> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#cluster> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#info> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#error> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "sims_abundance.error" ;
        cwl:stdout               "sims_abundance.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#cluster>
        rdfs:comment  "Optional input file(s), cluster mapping" ;
        sld:type      sld:null ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "--cluster" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "--cluster" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "--cluster" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStatsOut>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/rnaExpandLca>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaExpandLca> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/jobid>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#jobid> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#jobid>
        sld:type  xsd:string .

<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
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-c" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/protClustMap>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protClustMap> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protClustMap>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/clustMap>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaClustMap> ;
        cwl:valueFrom  "${ return [self]; }" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#expandSims> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protClustMap>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#md5index>
        rdfs:comment      "Optional input file, md5,seek,length" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--md5_index" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--md5_index" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--md5_index" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/output> .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/cluster> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/coverage> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/profileType> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/coverage>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#coverage> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#protLCA>
        rdfs:comment      "Input expanded protein LCA file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--prot" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#m5nrSCG>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protExpandLca>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/position>
        cwl:valueFrom  "${ return 2; }" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).650.contig.expand.lca" .

<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  "v1.2" ;
        cwl:arguments            ( [ cwl:valueFrom  "--verbose" ]
                                   [ CommandLineBinding:prefix  "--db" ;
                                     cwl:valueFrom              "$(runtime.tmpdir)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ cwl:valueFrom  "--verbose" ]
                                   [ CommandLineBinding:prefix  "--db" ;
                                     cwl:valueFrom              "$(runtime.tmpdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "uncluster_sims.py" ) ;
        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                             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/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/NetworkAccess> ] ;
        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:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "uncluster_sims.error" ;
        cwl:stdout               "uncluster_sims.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#filterSims> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#contigLCA>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/coverage>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#coverage> .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#profileType>
        rdfs:comment      "Profile type" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        sld:type          xsd:string .

<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" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--position" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile>
        rdfs:label  "Abundance Profile" ;
        cwl:in      <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/cluster> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/coverage> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/md5index> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/profileType> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/outName> ;
        cwl:out     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#sourceStats/profileType>
        cwl:valueFrom  "source" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#scgs>
        rdfs:comment      "md5 single copy gene file" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--scg" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/position>
        cwl:valueFrom  "${ return 2; }" .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaClustMap>
        sld:type  cwl:File .

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

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

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#coverage>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile>
        rdfs:label  "LCA Profile" ;
        cwl:in      <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/protClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/jobid> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/rnaClustMap> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/coverage> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/protExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/rnaExpandLca> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/m5nrSCG> ;
        cwl:out     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/contigLCA> ;
        cwl:run     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca>
        cwl:in   <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/profileType> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/input> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/coverage> ;
        cwl:out  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/rnaClustMap>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaClustMap> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protExpandLca> ;
        cwl:valueFrom  "$(self.basename).uncluster" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "create contig LCA from rRNA and Protein LCAs\n>find_contig_lca.py --rna <rnaLCA> --prot <protLCA> --scg <scgs> --output <outName>\n" ;
        rdfs:label               "contig LCA" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "--verbose" ]
                                 ) ;
        cwl:baseCommand          ( "find_contig_lca.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/find_contig_lca.tool.cwl#scgs> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#protLCA> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#outName> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#rnaLCA> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#output> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#error> , <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/find_contig_lca.tool.cwl#info> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stderr               "find_contig_lca.error" ;
        cwl:stdout               "find_contig_lca.log" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protExpandLca>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/uncluster_sims.tool.cwl#output>
        rdfs:comment       "Output unclustered similarity file" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.outName)" ] ;
        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/abundance-clca.workflow.cwl#lcaProfile/protExpandLca>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#protExpandLca> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#coverage>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortProt/input>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/output> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#expandLca/scgs>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#m5nrSCG> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#abundanceLca/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#jobid> ;
        cwl:valueFrom  "$(self).700.annotation.lca.abundance" .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#coverage>
        rdfs:comment      "Optional input file, assembly coverage" ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--coverage" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--coverage" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--coverage" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#lcaProfile/m5nrSCG>
        cwl:source  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#m5nrSCG> .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#sortRna/outName>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterRna/output> ;
        cwl:valueFrom  "$(self[0].basename).sort" .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Tools/sims_abundance.tool.cwl#input>
        rdfs:comment  "Input expanded sims file" ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-i" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-i" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] ;
        sld:type      [ cwl:inputBinding  [ CommandLineBinding:prefix
                                          "-i" ] ;
                        sld:items         cwl:File ;
                        sld:type          sld:array
                      ] .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#unclusterProt/clustMap>
        cwl:source     <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#protClustMap> ;
        cwl:valueFrom  "${ return [self]; }" .

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

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5index>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/contig-lca.workflow.cwl#rnaExpandLca>
        sld:type  cwl:File .

<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/Workflows/abundance-clca.workflow.cwl#md5Profile/profileType>
        cwl:valueFrom  "md5" .

<https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#rnaExpandLca>
        sld:type  cwl:File .

<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/abundance-clca.workflow.cwl#md5ProfileOut>
        cwl:outputSource  <https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/abundance-clca.workflow.cwl#md5Profile/output> ;
        sld:type          cwl:File .

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