Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c8ac3ed7209d6076dad937ef0e390d7b95c0fa8 https://github.com/galaxyproject/galaxy/commit/7c8ac3ed7209d6076dad937ef0e39... Author: Mataivic <victor.mataigne@wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Add a condition to FilterFailedDatasetsTool to remove empty files Hello, Here is an extra-condition for the tool ``FilterFailedDatasetsTool`` to allow it to remove empty datasets as well as failed datasets in a collection. I tested it on my data and it seems to work fine. Since it's my first time looking at galaxy's source code, I don't know if there is a proper way to do that ... And I didn't make the improvement for paired datasets because I don't have proper data to test it. But I assume it would be something like ``if forward_o.is_ok and reverse_o.is_ok and forward_o.has_data() and reverse_o.has_data():`` ? Commit: b27281aaedbf0dc26c8d577d20168e8592bdfc9c https://github.com/galaxyproject/galaxy/commit/b27281aaedbf0dc26c8d577d20168... Author: Mataivic <victor.mataigne@wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- improved filtering of empty files in a collection (1) - Supplemental parameter : 'remove_empty' which allow the user to choose if he/she wants to keep or not empty files in the collection. - Coming next : the modified wrapper. (Edited directly on GitHub). Commit: f4ec64a0057c81a62baf3874e3ac726f89fa86ac https://github.com/galaxyproject/galaxy/commit/f4ec64a0057c81a62baf3874e3ac7... Author: Mataivic <victor.mataigne@wanadoo.fr> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- modified wrapper filter_failed_collection - Supplemental 'select' parameter : 'remove_empty' Commit: 7c87dfdffda17b2cc6878e3a7dba9da9a70da45b https://github.com/galaxyproject/galaxy/commit/7c87dfdffda17b2cc6878e3a7dba9... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Simplify and modularize FilterFailedDatasetsTool class Commit: 8a4d18fba160aed43e15d2852093d6f8ded96dc9 https://github.com/galaxyproject/galaxy/commit/8a4d18fba160aed43e15d2852093d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_empty_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add filter empty collection tool I think having a separate tool for this task makes sense and makes the distinction between empty and fialed datasets clearer. Commit: babe2e5cc58502d9d0ba33fbd1ec0caf7a1c2b56 https://github.com/galaxyproject/galaxy/commit/babe2e5cc58502d9d0ba33fbd1ec0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Change get_new_elements to _get_new_elements And use same order for arguments in signature and caller. Commit: 46d8b318baac455ac3ff4c5782cfd9f6718e55bc https://github.com/galaxyproject/galaxy/commit/46d8b318baac455ac3ff4c5782cfd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Correct help text of filter_failed_collection and filter_empty_collection tools Commit: 0507818bbe3c712b506045458702122293780741 https://github.com/galaxyproject/galaxy/commit/0507818bbe3c712b5060454587021... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Add tests for filtering list:pair and list:list:pair collections Commit: 5992629619a39408f9e8a3082de96f1d73592f7c https://github.com/galaxyproject/galaxy/commit/5992629619a39408f9e8a3082de96... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Map over list or list:paired collection in filter collection tools Commit: 72dd53f55e7ae8ad3a18278da88cc800d7f6572e https://github.com/galaxyproject/galaxy/commit/72dd53f55e7ae8ad3a18278da88cc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-13 (Wed, 13 Jun 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Update comments to the fact that we're processing list or list:paired collections Commit: 02974b79c7a9d9cbe45b8ad08d7a532c11fcbe0b https://github.com/galaxyproject/galaxy/commit/02974b79c7a9d9cbe45b8ad08d7a5... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/filter_empty_collection.xml M lib/galaxy/tools/filter_failed_collection.xml M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5640 from Mataivic/patch-1 Add a FilterEmptyDatasetsTool and allow filtering tools to apply to arbitrary collection structures Compare: https://github.com/galaxyproject/galaxy/compare/db11a2549d33...02974b79c7a9 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.