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Merged
merged 3 commits into from
Aug 8, 2017
Merged

cleanup & simplification #18

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99efc30
cleanup & simplification
mr-c Aug 7, 2017
862c0f2
propagated @mr-c's stylistic changes to metadata_example.cwl
Aug 7, 2017
b87e79a
Misc cleanups
mr-c Aug 8, 2017
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28 changes: 11 additions & 17 deletions _includes/cwl/metadata_example.cwl
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Original file line number Diff line number Diff line change
@@ -1,34 +1,28 @@
#!/usr/bin/env cwl-runner

class: CommandLineTool
id: Example tool
label: Example tool
cwlVersion: v1.0
doc: |
An example tool demonstrating metadata.
class: CommandLineTool

requirements:
- class: ShellCommandRequirement
label: An example tool demonstrating metadata.

inputs:
bam_input:
aligned_sequences:
type: File
doc: The BAM file used as input
label: Aligned sequences in BAM format
format: edam:format_2572
inputBinding:
position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
report:
type: File
type: stdout
format: edam:format_1964
outputBinding:
glob: "*.txt"
doc: A text file that contains a line count

baseCommand: ["wc", "-l"]
label: A text file that contains a line count

$namespaces:
edam: http://edamontology.org/
edam: http://edamontology.org/
$schemas:
- http://edamontology.org/EDAM_1.18.owl
44 changes: 19 additions & 25 deletions _includes/cwl/metadata_example2.cwl
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Original file line number Diff line number Diff line change
@@ -1,55 +1,49 @@
#!/usr/bin/env cwl-runner

class: CommandLineTool
id: Example tool
label: Example tool
cwlVersion: v1.0
doc: |
An example tool demonstrating metadata. Note that this is an example and the metadata is not necessarily consistent.
class: CommandLineTool

requirements:
- class: ShellCommandRequirement
label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

inputs:
bam_input:
aligned_sequences:
type: File
doc: The BAM file used as input
label: Aligned sequences in BAM format
format: edam:format_2572
inputBinding:
position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
report:
type: File
type: stdout
format: edam:format_1964
outputBinding:
glob: "*.txt"
doc: A text file that contains a line count

baseCommand: ["wc", "-l"]

$namespaces:
s: https://schema.org/
edam: http://edamontology.org/

$schemas:
- https://schema.org/docs/schema_org_rdfa.html
label: A text file that contains a line count

s:author:
- class: s:Person
s:id: https://orcid.org/0000-0002-6130-1021
s:identifier: https://orcid.org/0000-0002-6130-1021
s:email: mailto:dyuen@oicr.on.ca
s:name: Denis Yuen

s:contributor:
- class: s:Person
s:id: http://orcid.org/0000-0002-7681-6415
s:identifier: http://orcid.org/0000-0002-7681-6415
s:email: mailto:briandoconnor@gmail.com
s:name: Brian O'Connor

s:citation: https://dx.doi.org/10.6084/m9.figshare.3115156.v2
s:codeRepository: https://github.com/common-workflow-language/common-workflow-language
s:dateCreated: "2016-12-13"
s:license: https://www.apache.org/licenses/LICENSE-2.0

$namespaces:
s: https://schema.org/
edam: http://edamontology.org/

$schemas:
- https://schema.org/docs/schema_org_rdfa.html
- http://edamontology.org/EDAM_1.18.owl
46 changes: 20 additions & 26 deletions _includes/cwl/metadata_example3.cwl
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Original file line number Diff line number Diff line change
@@ -1,55 +1,41 @@
#!/usr/bin/env cwl-runner

class: CommandLineTool
id: Example tool
label: Example tool
cwlVersion: v1.0
doc: |
An example tool demonstrating metadata. Note that this is an example and the metadata is not necessarily consistent.
class: CommandLineTool

requirements:
- class: ShellCommandRequirement
label: An example tool demonstrating metadata.
doc: Note that this is an example and the metadata is not necessarily consistent.

hints:
- class: ResourceRequirement
ResourceRequirement:
coresMin: 4

inputs:
bam_input:
aligned_sequences:
type: File
doc: The BAM file used as input
label: Aligned sequences in BAM format
format: edam:format_2572
inputBinding:
position: 1

baseCommand: [ wc, -l ]

stdout: output.txt

outputs:
report:
type: File
type: stdout
format: edam:format_1964
outputBinding:
glob: "*.txt"
doc: A text file that contains a line count

baseCommand: ["wc", "-l"]

$namespaces:
- s: https://schema.org/
- edam: https://edamontology.org/

$schemas:
- https://schema.org/docs/schema_org_rdfa.html
label: A text file that contains a line count

s:author:
- class: s:Person
s:id: https://orcid.org/0000-0002-6130-1021
s:identifier: https://orcid.org/0000-0002-6130-1021
s:email: mailto:dyuen@oicr.on.ca
s:name: Denis Yuen

s:contributor:
- class: s:Person
s:id: http://orcid.org/0000-0002-7681-6415
s:identifier: http://orcid.org/0000-0002-7681-6415
s:email: mailto:briandoconnor@gmail.com
s:name: Brian O'Connor

Expand All @@ -60,3 +46,11 @@ s:license: https://www.apache.org/licenses/LICENSE-2.0

s:keywords: edam:topic_0091 , edam:topic_0622
s:programmingLanguage: C

$namespaces:
s: https://schema.org/
edam: https://edamontology.org/

$schemas:
- https://schema.org/docs/schema_org_rdfa.html
- http://edamontology.org/EDAM_1.18.owl