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ProteinInferenceWorkflow.cwl
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ProteinInferenceWorkflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
MultipleInputFeatureRequirement: {}
inputs:
mztab_to_idxml_py: File
mztab: File
bait: string
fasta: File
idxml_output: string
missing_decoy_action:
type: string
default: "silent"
enzyme_specificity:
type: string
default: "full"
IL_equivalent:
type: boolean
default: TRUE
allow_unmatched:
type: boolean
default: TRUE
cp: File
compiler: string
xml_output: 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
# pia_genes_R: File
# bait: string
outputs:
pia_proteins:
type: File
outputSource: pia_proteins/proteins_csv
# pia_genes:
# type: File
# outputSource: pia_genes/genes_csv
steps:
mztab_to_idxml:
run: Tools/mztab_to_idxml.cwl
in:
mztab_to_idxml_py: mztab_to_idxml_py
mztab: mztab
bait: bait
out:
[idxml]
peptide_indexer:
run: Tools/peptide_indexer.cwl
in:
input: mztab_to_idxml/idxml
fasta: fasta
idxml_output: idxml_output
missing_decoy_action: missing_decoy_action
IL_equivalent: IL_equivalent
enzyme_specificity: enzyme_specificity
allow_unmatched: allow_unmatched
out:
[idxml]
pia_xml:
run: Tools/pia_xml.cwl
in:
cp: cp
compiler: compiler
idxml: peptide_indexer/idxml
bait: bait
xml_output: xml_output
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]
# [csv]
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]
# pia_genes:
# run: Tools/pia_genes.cwl
# in:
# pia_genes_R: pia_genes_R
# proteins_csv: pia_proteins/proteins_csv
# bait: bait
# out:
# [genes_csv]