Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b4c77b761799b3a8752a6fec500717b1a6f3818b https://github.com/galaxyproject/galaxy/commit/b4c77b761799b3a8752a6fec50071... Author: John Chilton jmchilton@gmail.com Date: 2015-11-18 (Wed, 18 Nov 2015)
Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py
Log Message: ----------- Introduce "Format 2" workflow definitions.
This is a slight tightening up of the ad-hoc, experimental workflow YAML definition used by the test framework (and by Kyle, but lets just admit Kyle is part of Galaxy's test framework).
This format is still defined entirely client side by transcoding the YAML or python object description into real (or format 1) Galaxy workflows - so these cannot realisticaly be declared part of Galaxy's public interface and can remain experimental and subject to change.
In addition to refactoring the code implementing these workflows for upstream modifications to explore new features, the format itself has been made slightly more stringent in two ways:
- 'steps' must now be explicit (previously converted auto-convert list to dict). - Ensure the workflow declared a 'class' is defined and the class is 'GalaxyWorkflow'.
This will help with discovery of workflow objects with downstream tooling (planemo for workflows?) and brings the Galaxy definition slightly more inline with the CWL definition for workflows (very slightly).
Commit: ab0829f2e8df480d467f3b575c18a1ace38543cd https://github.com/galaxyproject/galaxy/commit/ab0829f2e8df480d467f3b575c18a... Author: Martin Cech cech.marten@gmail.com Date: 2015-11-20 (Fri, 20 Nov 2015)
Changed paths: M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py A test/api/workflows_format_2/README.txt A test/api/workflows_format_2/__init__.py A test/api/workflows_format_2/converter.py A test/api/workflows_format_2/interface.py A test/api/workflows_format_2/main.py R test/api/yaml_to_workflow.py M test/functional/tools/simple_constructs.yml M test/unit/tools/test_parsing.py
Log Message: ----------- Merge pull request #1096 from jmchilton/format_2
Outline "Format 2" workflow definitions.
Compare: https://github.com/galaxyproject/galaxy/compare/a664deeee76b...ab0829f2e8df