cwlVersion: v1.1
class: Workflow
label: 'FragPipe: TMT Integrator and QC'
doc: |-
  This workflow step executes TMT-Integrator using the report tables generated by Philosopher. The program applies a series of statistical filters, and high-quality thresholds to filter the data. Summary report tables are created containing peptides, proteins, genes, and phosphosites (only for phospho-enriched data sets).
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requirements:
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- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement

inputs:
- id: psm_file
  type:
    type: array
    items: File
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  sbg:y: -238.8984375
- id: database
  type: File
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  sbg:y: -3.898444652557373

outputs:
- id: all_report_files
  type:
  - 'null'
  - type: array
    items: File
  outputSource:
  - tmt_integrator/all_report_files
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- id: tmt_qc_report
  label: TMT QC Report
  type:
  - 'null'
  - File
  outputSource:
  - tmt_integrator_qc/tmt_qc_report
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steps:
- id: tmt_integrator_qc
  label: TMT-Integrator QC
  in:
  - id: tmt_gene_report
    source: tmt_integrator/abundance_by_gene_report
  run: fragpipe-tmt-integrator-and-qc.cwl.steps/tmt_integrator_qc.cwl
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- id: tmt_integrator
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  in:
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    source:
    - psm_file
  - id: database
    source: database
  run: fragpipe-tmt-integrator-and-qc.cwl.steps/tmt_integrator.cwl
  out:
  - id: all_report_files
  - id: abundance_by_gene_report
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  sbg:y: -138

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sbg:categories:
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sbg:content_hash: ae0e5b97dd4fa1b912e0df5f4dc491c2e6c808735c5e97296e8d15f920a6d8e8f
sbg:contributors:
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sbg:createdBy: david.roberson
sbg:createdOn: 1618978230
sbg:id: |-
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sbg:image_url: |-
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sbg:links:
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sbg:modifiedBy: david.roberson
sbg:modifiedOn: 1618978230
sbg:original_source: |-
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sbg:project: david.roberson/build-fragpipe-proteomics-pipeline-tutorial
sbg:projectName: 'BUILD: FragPipe Proteomics Pipeline Tutorial'
sbg:publisher: sbg
sbg:revision: 0
sbg:revisionNotes: |-
  Uploaded using sbpack v2020.10.05. 
  Source: 
  repo: https://github.com/davidroberson/fragpipe-proteomics-pipeline-tutorial.git
  file: 
  commit: (uncommitted file)
sbg:revisionsInfo:
- sbg:modifiedBy: david.roberson
  sbg:modifiedOn: 1618978230
  sbg:revision: 0
  sbg:revisionNotes: |-
    Uploaded using sbpack v2020.10.05. 
    Source: 
    repo: https://github.com/davidroberson/fragpipe-proteomics-pipeline-tutorial.git
    file: 
    commit: (uncommitted file)
sbg:sbgMaintained: false
sbg:toolAuthor: Felipe da Veiga Leprevost
sbg:toolkit: FragPipe
sbg:toolkitVersion: v15.0
sbg:validationErrors: []
sbg:wrapperAuthor: Felipe da Veiga Leprevost; Dave Roberson