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