CWL User Guide 11: Advanced Inputs をやってみた

CWL User Guide 11: Advanced Inputs

Common Workflow Language User Guide: Advanced Inputs

今回は入力パラメータについて、高度な設定ができることが書かれています

この回にでてくる主なキーワード

• record

今回は、これまでとちがい、３ケースためしています。

• １つ目は、エラーになるケース
• ２つ目は、エラーにならないケース、排他的な指定
• ３つ目は、エラーにならないケース、２つ目の少し違う形のもの

CWLファイル、record.cwl

record.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
inputs:
  dependent_parameters:
    type:
      type: record
      name: dependent_parameters
      fields:
        itemA:
          type: string
          inputBinding:
            prefix: -A
        itemB:
          type: string
          inputBinding:
            prefix: -B
  exclusive_parameters:
    type:
      - type: record
        name: itemC
        fields:
          itemC:
            type: string
            inputBinding:
              prefix: -C
      - type: record
        name: itemD
        fields:
          itemD:
            type: string
            inputBinding:
              prefix: -D
outputs: []
baseCommand: echo

パラメータファイル１，record-job1.yml

record-job1.yml

dependent_parameters:
  itemA: one
exclusive_parameters:
  itemC: three

実行

実行方法

cwltool record.cwl record-job1.yml

実行結果1

$ cwltool record.cwl record-job2.yml
/usr/local/bin/cwltool 1.0.20171107133715
Resolved 'record.cwl' to 'file:///home/vagrant/cwl_user_guide_work/11-records/record.cwl'
record-job2.yml:6:3: invalid field `itemD`, expected one of: 'itemC'
[job record.cwl] /tmp/tmpxn1Gb8$ echo \
    -A \
    one \
    -B \
    two \
    -C \
    three
-A one -B two -C three
[job record.cwl] completed success
{}
Final process status is success

パラメータファイル２

record-job2.yml

dependent_parameters:
  itemA: one
  itemB: two
exclusive_parameters:
  itemC: three
  itemD: four

実行方法2

cwltool record.cwl record-job2.yml

実行結果2

$ cwltool record.cwl record-job2.yml
/usr/local/bin/cwltool 1.0.20171107133715
Resolved 'record.cwl' to 'file:///home/vagrant/cwl_user_guide_work/11-records/record.cwl'
record-job2.yml:6:3: invalid field `itemD`, expected one of: 'itemC'
[job record.cwl] /tmp/tmpxn1Gb8$ echo \
    -A \
    one \
    -B \
    two \
    -C \
    three
-A one -B two -C three
[job record.cwl] completed success
{}
Final process status is success

パラメータファイル3

record-job3.yml

dependent_parameters:
  itemA: one
  itemB: two
exclusive_parameters:
  itemD: four

実行方法3

cwltool record.cwl record-job3.yml

実行結果3

$ cwltool record.cwl record-job3.yml
/usr/local/bin/cwltool 1.0.20171107133715
Resolved 'record.cwl' to 'file:///home/vagrant/cwl_user_guide_work/11-records/record.cwl'
[job record.cwl] /tmp/tmp5enbk2$ echo \
    -A \
    one \
    -B \
    two \
    -D \
    four
-A one -B two -D four
[job record.cwl] completed success
{}
Final process status is success

今回使ったファイル

cwl_user_guide_work/11-records at master · manabuishii/cwl_user_guide_work