/
TransDecoder-v5-wf-2steps.cwl
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TransDecoder-v5-wf-2steps.cwl
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class: Workflow
cwlVersion: v1.0
label: >-
TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed
by TransDecoder.Predict (step2)
$namespaces:
edam: 'http://edamontology.org/'
s: 'http://schema.org/'
inputs:
- id: singleBestOnly
type: boolean?
- format: edam:format_1929 # FASTA
id: transcriptsFile
type: File
- format: 'edam:format_3475'
id: geneToTranscriptMap
type: File?
- id: geneticCode
type: ../tools/TransDecoder/TransDecoder-v5-genetic_codes.yaml#genetic_codes?
- id: minimumProteinLength
type: int?
- id: strandSpecific
type: boolean?
- id: noRefineStarts
type: boolean?
- id: retainBlastpHits
type: string?
- id: retainLongOrfsLength
type: int?
- id: retainLongOrfsMode
type: string?
- id: retainPfamHits
type: string?
- id: train
type: int?
outputs:
- id: bed_output
outputSource:
- predict_coding_regions/bed_output
type: File
- id: coding_regions
outputSource:
- predict_coding_regions/coding_regions
type: File
- id: gff3_output
outputSource:
- predict_coding_regions/gff3_output
type: File
- id: peptide_sequences
outputSource:
- predict_coding_regions/peptide_sequences
type: File
steps:
- id: extract_long_orfs
in:
- id: transcriptsFile
source: transcriptsFile
- id: geneToTranscriptMap
source: geneToTranscriptMap
- id: geneticCode
source: geneticCode
- id: minimumProteinLength
source: minimumProteinLength
- id: strandSpecific
source: strandSpecific
out:
- id: workingDir
run: ../tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl
label: Extracts the long open reading frames
- id: predict_coding_regions
in:
- id: longOpenReadingFrames
source: extract_long_orfs/workingDir
- id: singleBestOnly
source: singleBestOnly
- id: noRefineStarts
source: noRefineStarts
- id: retainBlastpHits
source: retainBlastpHits
- id: retainLongOrfsLength
source: retainLongOrfsLength
- id: retainLongOrfsMode
source: retainLongOrfsMode
- id: retainPfamHits
source: retainPfamHits
- id: train
source: train
- id: transcriptsFile
source: transcriptsFile
out:
- id: bed_output
- id: coding_regions
- id: gff3_output
- id: peptide_sequences
run: ../tools/TransDecoder/TransDecoder.Predict-v5.cwl
label: Predicts the likely coding regions
requirements:
- class: SchemaDefRequirement
types:
- $import: ../tools/TransDecoder/TransDecoder-v5-genetic_codes.yaml
$schemas:
- 'http://edamontology.org/EDAM_1.16.owl'
- 'https://schema.org/docs/schema_org_rdfa.html'
's:copyrightHolder': 'EMBL - European Bioinformatics Institute, 2018'
's:license': 'https://www.apache.org/licenses/LICENSE-2.0'
's:author': Maxim Scheremetjew