Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e79c8c77e29f0aa5e6377d77ffa68d808ca4c89 https://github.com/galaxyproject/galaxy/commit/1e79c8c77e29f0aa5e6377d77ffa6... Author: Mark Einon mark.einon@gmail.com Date: 2016-02-04 (Thu, 04 Feb 2016)

Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py

Log Message: ----------- Optionally pass dataset lists as a single file within tool wrappers

This change introduces an extra boolean XML attribute 'pass_as_file', that when used with an input parameter already having the 'multiple=True' attribute, passes the dataset list of files to the wrapped program as a single file containing a list of the dataset files.

Commit: 27618a319d9c3bac01484bad80494f4423c04673 https://github.com/galaxyproject/galaxy/commit/27618a319d9c3bac01484bad80494... Author: Mark Einon mark.einon@gmail.com Date: 2016-02-04 (Thu, 04 Feb 2016)

Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/wrappers.py

Log Message: ----------- [Trivial] Whitespace fixes to please pylint

Commit: 66350fb87100a8986a95c28f9b532564c98f0034 https://github.com/galaxyproject/galaxy/commit/66350fb87100a8986a95c28f9b532... Author: Mark Einon mark.einon@gmail.com Date: 2016-02-04 (Thu, 04 Feb 2016)

Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Modify pass_as_file to apply to all Multiple parameters and add test case

Change the pass_as_file XML attribute to a cheetah method call, and apply to all paramter types that can have Multiple=True set - those given in DatasetListWrappers and DatasetCollectionWrappers.

Test case and modification suggestion provided by John Chilton jmchilton@gmail.com

Commit: 75f1b58ecb8a4e60fd9f3bbcbc6b9501005b903d https://github.com/galaxyproject/galaxy/commit/75f1b58ecb8a4e60fd9f3bbcbc6b9... Author: Martin Cech cech.marten@gmail.com Date: 2016-02-05 (Fri, 05 Feb 2016)

Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/wrappers.py A test/functional/tools/paths_as_file.xml M test/functional/tools/samples_tool_conf.xml

Log Message: ----------- Merge pull request #1658 from einon/pass_lists_as_file

Optionally pass dataset lists as a single file within tool wrappers

Compare: https://github.com/galaxyproject/galaxy/compare/dfceb5c144de...75f1b58ecb8a