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msconvert_workflow_main.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: For conversion purpose
inputs:
in_file:
type: File
label: mzXML or vendor file format
format: edam:format_3245
in_file1:
type: File
in_file2:
type: File
# parameters:
# type: string[]
# default: [mzML]
steps:
step1:
run: string_extractor.cwl
in:
input_file: in_file
out: [output, output2, output3, output4, output5]
step2:
run: msconvert.cwl
in:
in_file1: in_file1
in_file: in_file
in_file2: in_file2
in_dir: step1/output2
out: [output_dir]
step3:
run: validation_file_creation.cwl
in:
input: step1/output3
in_dir: step1/output2
input2: step1/output5
out: [output_dir]
outputs:
outputA:
type: string
outputSource: step1/output
outputB:
type: string
outputSource: step1/output4
outputC:
type: Directory
outputSource: step2/output_dir
outputD:
type: Directory
outputSource: step3/output_dir
$namespaces:
s: https://schema.org/
edam: http://edamontology.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf
- http://edamontology.org/EDAM_1.18.owl