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

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mass_tolerance> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#unimod_path> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv_py> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster_py> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_R> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mod_csv> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/mass_tolerance>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mass_tolerance> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "python3" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#mztab_to_csv_py> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#mztab> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#csv> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#bait>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mass_tolerance>
        cwl:default  "50" ;
        sld:type     xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "python3" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#unimod_path> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#tol_py_csv> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#modifications_faster_py> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#mod_csv> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#bait>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#mod_csv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bait)_mod.csv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/bait>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#bait> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#modifications_R>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/modifications_R>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_R> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/bait>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#bait> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#mass_tolerance>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#modifications_faster_py>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#mztab>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#unimod_path>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications>
        cwl:in   <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/csv> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/modifications_R> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/mass_tolerance> ;
        cwl:out  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/tol_py_csv> ;
        cwl:run  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_R>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#tol_py_csv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bait)_tol_py.csv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#bait>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster>
        cwl:in   <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/modifications_faster_py> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/tol_py_csv> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/unimod_path> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/bait> ;
        cwl:out  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/mod_csv> ;
        cwl:run  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "Rscript" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#mass_tolerance> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#modifications_R> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#csv> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#tol_py_csv> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/mztab>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv>
        cwl:in   <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/bait> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/mztab> , <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/mztab_to_csv_py> ;
        cwl:out  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/csv> ;
        cwl:run  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster_py>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/unimod_path>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#unimod_path> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mod_csv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/mod_csv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#unimod_path>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/mztab_to_csv_py>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv_py> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv_py>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/bait>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#bait> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/csv>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#mztab_to_csv/csv> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/modifications_faster_py>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster_py> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications.cwl#csv>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#bait>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#mztab_to_csv_py>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications_faster/tol_py_csv>
        cwl:source  <https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Modification_workflow.cwl#modifications/tol_py_csv> .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/modifications_faster.cwl#tol_py_csv>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/57b4fbb3579e17ec414ba96fbbfb332f1740d62b/Tools/mztab_to_csv.cwl#csv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bait).csv" ] ;
        sld:type           cwl:File .