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Protein_Inference_workflow.cwl
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Protein_Inference_workflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
inputs:
cp: File
compiler: string
idxml: File
outfile: string
name:
type: string
default: "test"
jar: File
proteinExport: string
paramFile: File
fileType:
type: string
default: "mzTab"
mztab_to_csv_py: File
pia_proteins_R: File
bait: string
outputs:
proteins_csv:
type: File
outputSource: pia_proteins/proteins_csv
steps:
pia_xml:
run: Tools/pia_xml.cwl
in:
cp: cp
compiler: compiler
idxml: idxml
bait: bait
outfile: outfile
name: name
out:
[xml]
pia_run:
run: Tools/pia_run.cwl
in:
jar: jar
xml: pia_xml/xml
bait: bait
fileType: fileType
paramFile: paramFile
proteinExport: proteinExport
out:
[mztab]
mztab_to_csv:
run: Tools/mztab_to_csv.cwl
in:
mztab_to_csv_py: mztab_to_csv_py
mztab: pia_run/mztab
bait: bait
out:
[csv]
pia_proteins:
run: Tools/pia_proteins.cwl
in:
pia_proteins_R: pia_proteins_R
csv: mztab_to_csv/csv
bait: bait
out:
[proteins_csv]