CWL User Guide 19: Custom Types

Common Workflow Language User Guide: Custom Types

18はないようです。

今回は、独自の type を定義して CWL で使う方法について書かれています

Key Points を引用すると

You can create your own custom types to load into descriptions.
These custom types allow the user to configure the behaviour of a tool without tinkering directly with the tool description.
Custom types are described in separate YAML files and imported as needed.

この回にでてくる主なキーワード

inputs:applications
requirements:SchemaDefRequirement
ResourceRequirement

CWLファイル、custom-types.cwl

custom-types.cwl

cwlVersion: v1.0
class: CommandLineTool

label: "InterProScan: protein sequence classifier"

doc: |
      Version 5.21-60 can be downloaded here:
      https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload

      Documentation on how to run InterProScan 5 can be found here:
      https://github.com/ebi-pf-team/interproscan/wiki/HowToRun

requirements:
  ResourceRequirement:
    ramMin: 10240
    coresMin: 3
  SchemaDefRequirement:
    types:
      - $import: InterProScan-apps.yml

hints:
  SoftwareRequirement:
    packages:
      interproscan:
        specs: [ "https://identifiers.org/rrid/RRID:SCR_005829" ]
        version: [ "5.21-60" ]

inputs:
  proteinFile:
    type: File
    inputBinding:
      prefix: --input
  applications:
    type: InterProScan-apps.yml#apps[]?
    inputBinding:
      itemSeparator: ','
      prefix: --applications

baseCommand: interproscan.sh

arguments:
 - valueFrom: $(inputs.proteinFile.nameroot).i5_annotations
   prefix: --outfile
 - valueFrom: TSV
   prefix: --formats
 - --disable-precalc
 - --goterms
 - --pathways
 - valueFrom: $(runtime.tmpdir)
   prefix: --tempdir


outputs:
  i5Annotations:
    type: File
    format: iana:text/tab-separated-values
    outputBinding:
      glob: $(inputs.proteinFile.nameroot).i5_annotations

$namespaces:
 iana: https://www.iana.org/assignments/media-types/
 s: http://schema.org/
$schemas:
 - https://schema.org/docs/schema_org_rdfa.html

s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"

パラメータファイル

custom-types.yml

proteinFile:
    class: File
    path: test_proteins.fasta

必要なファイル

InterProScan-apps.yml

type: enum
name: apps
symbols:
 - TIGRFAM
 - SFLD
 - SUPERFAMILY
 - Gene3D
 - Hamap
 - Coils
 - ProSiteProfiles
 - SMART
 - CDD
 - PRINTS
 - PIRSF
 - ProSitePatterns
 - Pfam
 - ProDom
 - MobiDBLite

test_proteins.fastaの取得について

実行

実行方法

実行結果

現在の状態では
interproscan.sh がないってことで、エラーになっています。
これについては問い合わせ予定。

$ cwltool custom-types.cwl custom-types.yml
/usr/local/bin/cwltool 1.0.20171107133715
Resolved 'custom-types.cwl' to 'file:///home/vagrant/cwl_user_guide_work/19-custom-types/custom-types.cwl'
custom-types.cwl:1:1: unrecognized extension field `http://schema.org/license`.  Did you include a $schemas section?
custom-types.cwl:1:1: unrecognized extension field `http://schema.org/copyrightHolder`.  Did you include a $schemas section?
[job custom-types.cwl] /tmp/tmpNxr2ff$ interproscan.sh \
    --outfile \
    test_proteins.i5_annotations \
    --formats \
    TSV \
    --disable-precalc \
    --goterms \
    --pathways \
    --tempdir \
    /tmp/tmph91Fgl \
    --input \
    /tmp/tmpJFLLEi/stg9a4b13fb-77ed-4d7c-991b-401d4dc78a1b/test_proteins.fasta
'interproscan.sh' not found
[job custom-types.cwl] completed permanentFail
{}
Final process status is permanentFail

今回使ったファイル

cwl_user_guide_work/19-custom-types at master · manabuishii/cwl_user_guide_work