Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 914adfcc0cd5e8b060df059da9a4f8e9b1293fde https://github.com/galaxyproject/galaxy/commit/914adfcc0cd5e8b060df059da9a4f... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Sychronize tool shed, planemo, and toolbox code for filtering out non-tool XML files. A single abstraction will allow toolbox and planemo to deal with other kinds of tools in the future, and the stronger preconditions should eliminate some busy error logging when monitoring a tool directory. Commit: 20b47f3ca208ded3682f68591f5801b85547efc1 https://github.com/galaxyproject/galaxy/commit/20b47f3ca208ded3682f68591f580... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update looks_like_a_tool to respect enable_beta_tool_formats. Default is off obviously, so for instance the tool shed will never think unsupported beta tools are real tools. Commit: a8ed6146e88642b17273e316c571c5a5a9f4df45 https://github.com/galaxyproject/galaxy/commit/a8ed6146e88642b17273e316c571c... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/util/odict.py Log Message: ----------- Tweak YAML tools to use ordered dictionaries. Order of inputs and outputs in Galaxy is important, so preserve this order if using dictionary-style (both available) for inputs and/or outputs. Commit: b7b8f097d5a7617b2997f254b4e0229adfaae623 https://github.com/galaxyproject/galaxy/commit/b7b8f097d5a7617b2997f254b4e02... Author: John Chilton <jmchilton@gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Enhance YAML/dictionary tool rep. to allow output collections. Commit: f874d559b7db28c3fa7b4df6844f077da419911a https://github.com/galaxyproject/galaxy/commit/f874d559b7db28c3fa7b4df6844f0... Author: Martin Cech <cech.marten@gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/odict.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #1368 from jmchilton/looks_like_a_tool Unify and Abstract Code for Checking if File Looks Like a Tool Compare: https://github.com/galaxyproject/galaxy/compare/ae2b94824a32...f874d559b7db