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Update CWL documentation to include container information...

... to demonstrate and so the linting now passes.
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jmchilton committed May 6, 2016
1 parent a4e6958 commit 4cd571c3d20e1f8be0347ad23a6e44bda1dab393
Showing with 11 additions and 8 deletions.
  1. +7 −8 docs/_writing_cwl_intro.rst
  2. +1 −0 docs/writing/gen.sh
  3. +3 −0 docs/writing/seqtk_seq_v3.cwl
@@ -62,7 +62,8 @@ tool is generated.
--name 'Convert to FASTA (seqtk)' \
--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
--example_input 2.fastq \
--example_output 2.fasta
--example_output 2.fasta \
--container 'dukegcb/seqtk' \
--help_from_command 'seqtk seq'

This command generates the following CWL YAML file.
@@ -82,16 +83,14 @@ This command generates the following CWL YAML file.
.. CHECK: Tool defines an id [seqtk_seq_v3].
Applying linter cwl_validation... CHECK
.. INFO: CWL appears to be valid.
Applying linter docker_image... WARNING
.. WARNING: Tool does not specify a DockerPull source.
Applying linter docker_image... CHECK
.. INFO: Tool will run in Docker image [dukegcb/seqtk].
Applying linter new_draft... CHECK
.. INFO: Modern CWL version [cwl:draft-3]
Failed linting

Here the linting failed because we have not yet defined a Docker image for the
the tool. A later revision of this document will cover specifying a Docker image
for this tool with the ``--container`` argument and discuss defining more
parameters for this tool.
A later revision of this document ill discuss defining more
parameters for this tool and include information on generating and
running tests with planemo for CWL tools.

For more information on the Common Workflow Language check out the Draft 3
`User Guide`_ and Specification_.
@@ -42,5 +42,6 @@ planemo tool_init --force \
--example_command 'seqtk seq -a 2.fastq > 2.fasta' \
--example_input 2.fastq \
--example_output 2.fasta \
--container 'dukegcb/seqtk' \
--help_from_command 'seqtk seq'
mv seqtk_seq.cwl seqtk_seq_v3.cwl
@@ -3,6 +3,9 @@ cwlVersion: 'cwl:draft-3'
class: CommandLineTool
id: "seqtk_seq"
label: "Convert to FASTA (seqtk)"
requirements:
- class: DockerRequirement
dockerPull: dukegcb/seqtk
inputs:
- id: input1
type: File

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