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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs>
        rdfs:label  "Convert final protein seqid list to XML jobs" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/taxid> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/output_seqids> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/lds2>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_lds2.basename)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.in_lds2.basename)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/axml> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/text_only> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/out> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/oseqids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oseqids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#text_only>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-text-only" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/oproteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oproteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#input> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oseqids>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/it>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-it" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-it" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#pplacer_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-pplacer-path" ] ;
        sld:default       "/usr/local/pplacer/1.1a18" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#local>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-local" ] ;
        sld:default       true ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/nogenbank>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#nogenbank> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "This workflow is specialized for the simple case of XML input that just need a little bit of massaging.\nWe need to have a flavored file because gpx_qsubmit reacts on the presence of a particular form of input instead of relying on a presence of actual non-empty container of objects\n" ;
        rdfs:label               "gpx_qsubmit" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "gpx_qsubmit" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl#xml_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl#output_xml_jobs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl#jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/input>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-input" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxid>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_results>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/output> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm>
        rdfs:label  "Run CheckM" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_data_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/assm_to_prots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/filter_for_raw_checkm> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/proteins> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_results> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_raw> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#checkm_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-checkm-path" ] ;
        sld:default       "/root/venv/bin" ;
        sld:type          xsd:string , sld:null .

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

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "checkm_wnode" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#checkm_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#checkm_data_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#output_dir> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#pplacer_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#hmmsearch_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#input_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#seqids> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#outdir> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.proteins)"
                                                ] ;
                                   cwl:listing  [ Dirent:writable  false ;
                                                  cwl:entry        "$(inputs.seqids)"
                                                ]
                                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#axml>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-axml" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/it>
        sld:default  true .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "checkm_wnode" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#assm_to_prots> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_data_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#filter_for_raw_checkm> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#taxon_db> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_raw> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_results> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#models>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/lds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/in_lds2>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#filter_for_raw_checkm>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gpx_qdump" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-produce-empty-file" ) ;
        cwl:baseCommand          ( "gpx_qdump" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/text_only>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/nogenbank>
        sld:default  true .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/output> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "protein_extract" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#olds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#it> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oseqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#nogenbank> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/oproteins>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "proteins.asn" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#out>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.out_name)" ] ;
        sld:type           cwl:File .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/checkm_data_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/input_jobs> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/outdir> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/input_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/outdir> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#lds2>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/nogenbank>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-nogenbank" ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#olds2>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_raw>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/out> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#nogenbank>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl#output_xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-o" ] ;
        sld:default       "jobs.xml" ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#it>
        sld:type  xsd:boolean , sld:null .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/in_lds2> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/lds2> ;
        cwl:run  [ a                 cwl:CommandLineTool ;
                   cwl:baseCommand   ( "sqlite3" ) ;
                   cwl:baseCommand   ( "sqlite3" ) ;
                   cwl:inputs        <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/in_lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/sql> ;
                   cwl:outputs       <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/lds2> ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  [ Dirent:writable  true ;
                                                      cwl:entry        "$(inputs.in_lds2)"
                                                    ]
                                     ] ;
                   cwl:requirements  [ a            cwl:InitialWorkDirRequirement ;
                                       cwl:listing  [ Dirent:writable  true ;
                                                      cwl:entry        "$(inputs.in_lds2)"
                                                    ]
                                     ]
                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/taxid>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxid> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/it>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#it> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/seqids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.oseqids)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.oseqids)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#output_seqids_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-output-seqids" ] ;
        sld:default       "annotation.seqids" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/it> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/olds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/oproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/oseqids> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/proteins> ;
        cwl:run  [ a                cwl:CommandLineTool ;
                   cwl:baseCommand  ( "protein_extract" ) ;
                   cwl:baseCommand  ( "protein_extract" ) ;
                   cwl:inputs       <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/it> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/oproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/olds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/oseqids> ;
                   cwl:outputs      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/lds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/proteins>
                 ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/lds2> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#output_seqids>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_seqids_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit/xml_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#assm_to_prots> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "xmlformat" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#out_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#entry_point_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#text_only> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#input> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#axml> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#out> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "" ;
                                                  cwl:entryname  "empty"
                                                ]
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#out_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-out" ] ;
        sld:default       "checkm.txt" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#lds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-lds2" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/olds2>
        sld:default  "checkm.LDS2" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl#xml_jobs>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-xml-jobs" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/assm_to_prots>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#taxid>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxid" ] ;
        sld:type          xsd:int .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#proteins>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/proteins> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#checkm_data_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-checkm-data-path" ] ;
        sld:type          cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#xmlformat/axml>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#filter_for_raw_checkm> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/in_lds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/lds2> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/seqids> .

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

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/lds2>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.olds2)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.olds2)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#input>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#seqids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/olds2>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#olds2> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_raw>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_raw> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#proteins>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/filter_for_raw_checkm>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#filter_for_raw_checkm> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/xmlformat.cwl#entry_point_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-entry-point" ] ;
        sld:default       "empty" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl#unzip>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-unzip" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#filter_for_raw_checkm>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/olds2>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-olds2" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-olds2" ] ;
        sld:default       "LDS2" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#taxon_db>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-taxon-db" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/proteins>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/proteins> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_data_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_data_path> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_data_path>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/unzip>
        sld:default  "*" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#assm_to_prots>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/checkm_wnode.cwl#hmmsearch_path>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-hmmsearch-path" ] ;
        sld:default       "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/bin" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/taxon_db>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxon_db> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#lds2_fix/run/sql>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:default       "update file set file_name=replace(file_name, rtrim(file_name, replace(file_name, '/', '')), '');" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/oproteins>
        sld:default  "proteins-for-checkm.asn" .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/seqids>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs/output_seqids> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins>
        rdfs:label  "Extract final proteins" ;
        cwl:in      <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/nogenbank> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/it> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/olds2> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/oproteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/input> ;
        cwl:out     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/lds2> ;
        cwl:run     <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl> .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit/xml_jobs> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit/jobs> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qsubmit_proteins_xml.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/checkm_data_path>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_data_path> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#seqids>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/seqids> ;
        sld:type          cwl:File .

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

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "checkm" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#convert_seqids_to_jobs> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm> ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxon_db> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_data_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#filter_for_raw_checkm> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#models> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxid> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_results> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_raw> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_wnode/input_jobs>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qsubmit/jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#oproteins>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "proteins_for_checkm" ) ;
        cwl:cwlVersion           cwl:v1.2 ;
        cwl:inputs               <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#output_seqids_name> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#local> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#taxid> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#jobs_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#output_seqids> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/proteins_for_checkm.cwl#jobs> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#taxon_db>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#extract_final_proteins/input>
        cwl:source  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#models> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#checkm_results>
        cwl:outputSource  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/checkm/wf_checkm.cwl#run_checkm/checkm_results> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#checkm_data_path>
        sld:type  cwl:Directory .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump>
        cwl:in   <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/input_path> , <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/unzip> ;
        cwl:out  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/task_types/tt_checkm_wnode.cwl#gpx_qdump/output> ;
        cwl:run  <https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/gpx_qdump.cwl> .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/oseqids>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-oseqids" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-oseqids" ] ;
        sld:default       "proteins.seq_ids" ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/681555881cbdf95a1f4c29f6dc272eb6ca8e4d60/progs/protein_extract.cwl#protein_extract/run/proteins>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.oproteins)" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.oproteins)" ] ;
        sld:type           cwl:File .