Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5d404c912340013aab34fe3350a2570010b0898 https://github.com/galaxyproject/galaxy/commit/d5d404c912340013aab34fe3350a2... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-29 (Tue, 29 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement special config file to dump parameters as json. ``` <configfiles> <inputs name="inputs" format="json" version="1" /> </configfiles> ``` Version is specified as 1, because the Galaxy tool plumbing doesn't really distinguish between parameter is '', parameter was explicitly supplied as None, parameter was absent, etc... - everything is a just a string in some ways. This distinction may be more important with JSON and for instance the CWL will require more percision, so we may want to revise Galaxy's tool handling in a backward compatible way someday. Commit: de0c913b8bb3ca01fd0ab5c8286450dbef9b604d https://github.com/galaxyproject/galaxy/commit/de0c913b8bb3ca01fd0ab5c828645... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/wrapped_json.py M test/functional/tools/inputs_as_json.xml Log Message: ----------- More work on converting tool inputs to json. - Drop version requirement per commends by @bgruening. - Add examples for conditionals, repeats, sections, colors, and booleans specified truevalue/falsevalue. - Various bug fixes unearthed by new test cases. Commit: cd32b91dc9f562d17349d8cc15ba1b60eba07f70 https://github.com/galaxyproject/galaxy/commit/cd32b91dc9f562d17349d8cc15ba1... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M test/functional/tools/inputs_as_json.xml Log Message: ----------- Update inputs_as_json.xml to drop version attribute. Also add note about filename. Commit: 9a0ef0ed14893bf1dcaae67b466a8b1167571032 https://github.com/galaxyproject/galaxy/commit/9a0ef0ed14893bf1dcaae67b466a8... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/parameters/wrapped_json.py Log Message: ----------- Expose hidden parameters in inputs json. Commit: 2b2f93d393a4e66c0e466e98a945222bd54e448a https://github.com/galaxyproject/galaxy/commit/2b2f93d393a4e66c0e466e98a9452... Author: Eric Rasche <rasche.eric@gmail.com> Date: 2015-12-30 (Wed, 30 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py A lib/galaxy/tools/parameters/wrapped_json.py A test/functional/tools/inputs_as_json.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1405 from jmchilton/json_config Implement special config file to dump parameters as json. Compare: https://github.com/galaxyproject/galaxy/compare/14a618ee3ab0...2b2f93d393a4