@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix Parameter: <https://w3id.org/cwl/cwl#Parameter/> .
@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 ns2:   <http://schema.org/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep/hits>
        cwl:source  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#table_hits> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords/infernal_matches>
        cwl:source  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep/SSUs> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl#SSUs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "SSUs" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl#matched_seqs_with_coords>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "matched_seqs_with_coords" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords>
        cwl:in   <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords/infernal_matches> ;
        cwl:out  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords/matched_seqs_with_coords> ;
        cwl:run  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl#infernal_matches>
        rdfs:label            "output from infernal cmscan or cmsearch" ;
        Parameter:streamable  true ;
        sld:type              cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#table_hits>
        rdfs:label  "output of infernal's cmscan or cmsearch" ;
        sld:type    cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        ns2:copyrightHolder      "EMBL - European Bioinformatics Institute" ;
        ns2:license              "https://www.apache.org/licenses/LICENSE-2.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords> , <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/NetworkAccess> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/LoadListingRequirement> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#table_hits> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#SSU_coordinates> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#SSU_coordinates>
        cwl:outputSource  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#extract_coords/matched_seqs_with_coords> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "The awk script takes the output of Infernal's cm{scan,search} fmt=2 mode and\nmakes it suitable for use by esl-sfetch, a sequence selector\n\nReading the user's guide for Infernal, Version 1.1.2; July 2016\nhttp://eddylab.org/infernal/Userguide.pdf#page=60 we see that\nthe relevant fields in the cmscan output are:\n(fmt2 column number: explanation)\n3: The accession of the target sequence or profile, or ’-’ if none\n4: The name of the query sequence or profile \n10: The start of the alignment of this hit with respect to the\n    sequence, numbered 1..L for a sequence of L residues.\n11: The end of the alignment of this hit with respect to the sequence,\n    numbered 1..L for a sequence of L residues\n\nLikewise the format esl-sfetch wants is: <newname> <from> <to> <source seqname>\n\nPutting it all together we see that the newname (which esl-sfetch with\noutput using) is a concatenation of the original name, the sequence\nnumber, and the coordinates.\n" ;
        ns1:original_cwlVersion  "v1.0" ;
        ns2:copyrightHolder      "EMBL - European Bioinformatics Institute" ;
        ns2:license              "https://www.apache.org/licenses/LICENSE-2.0" ;
        cwl:arguments            ( "{print $4\"-\"$3\"/\"$10\"-\"$11\" \"$10\" \"$11\" \"$4}" "$(inputs.infernal_matches.path)" ) ;
        cwl:baseCommand          ( "awk" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl#infernal_matches> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/extract-coords-from-cmscan.cwl#matched_seqs_with_coords> ;
        cwl:stdout               "matched_seqs_with_coords" .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep>
        cwl:in   <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep/hits> ;
        cwl:out  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/SSU-from-tablehits.cwl#grep/SSUs> ;
        cwl:run  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl> .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl#hits>
        Parameter:streamable  true ;
        sld:type              cwl:File .

<https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        ns2:copyrightHolder      "EMBL - European Bioinformatics Institute" ;
        ns2:license              "https://www.apache.org/licenses/LICENSE-2.0" ;
        cwl:arguments            ( "$(inputs.hits.path)" ) ;
        cwl:baseCommand          ( "grep" "SSU" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/v1.2> ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/LoadListingRequirement> ] ;
        cwl:hints                [ a  <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/NetworkAccess> ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl#hits> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/56dafa4dab5892c5afa35713563dddc78ec5a00d/tools/pull-SSUs.cwl#SSUs> ;
        cwl:stdout               "SSUs" .