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More generalized planemo testing enhancements. #491

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merged 9 commits into from Jun 15, 2016

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cwl enhancement testing tools workflows
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  Planemo as a Work...
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@jmchilton @nsoranzo
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jmchilton commented May 31, 2016

  • Allow job to be embedded in -tests.yml artifacts - in addition to referencing job descriptions by file path.
  • Allow building CWL test cases from example commands - tool_init can now respect --test_case and --cwl at the same time.
  • Update CWL introduction docs to demonstrate building a test case and include a description of how to run it.
  • Update CWL introduction docs to demonstrate serving a CWL tool with Galaxy.

Fixes #476 (except producing XUnit reports).

jmchilton added some commits May 26, 2016

@jmchilton
Fix for output json.
cf5e059
@jmchilton
More testing of outputs - now using galaxy-lib... 
... for shared functionality between testing inside Galaxy's test framework and planemo driven testing.

CWL and workflow tests now can specify more checksum types, a file to compare against, a method for comparison ('diff', 're_match', 're_match_multiline', 'sim_size', and 'contains') as well as other options such as 'sort', 'line_diff', etc....

xref #476
b2135cb
@jmchilton
Fix test report ID parsing for non-Galaxy tool artifacts.
4b14e62
@jmchilton
More generalized planemo testing enhancements. 
 - Allow job to be embedded in `-tests.yml` artifacts - in addition to referncing job descriptions by file path.
 - Allow building CWL test cases from example commands - tool_init can now respect --test_case and --cwl at the same time.
 - Update CWL introduction docs to demonstrate building a test case and include a description of how to run it.
 - Update CWL introduction docs to demonstrate serving a CWL tool with Galaxy.

Fixes #476.
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@jmchilton jmchilton added enhancement testing cwl workflows tools labels May 31, 2016

@jmchilton jmchilton added this to the Planemo as a Workflow SDK milestone May 31, 2016

docs/_writing_cwl_intro.rst Outdated
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.
In addition to the file actual tool file, a test file will be generated

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nsoranzo Jun 1, 2016

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s/file actual tool file/actual tool file/

@jmchilton jmchilton force-pushed the jmchilton:galaxy_style_testing_syntax branch from a191e97 to 5c1002c Jun 7, 2016

@jmchilton jmchilton merged commit 72f6740 into galaxyproject:master Jun 15, 2016
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