Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a2e0e6ba6c404aa899a91817ccf091b9a8fcecfa https://github.com/galaxyproject/galaxy/commit/a2e0e6ba6c404aa899a91817ccf09... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/merge_collection.xml Log Message: ----------- Initial commit for new 'Merge Collection' tool. Tool takes two input list collection and combined them together into a single unified list. Tool provides options on how to deal when element_identifier are found in both list Commit: a76960b9a6523376e8d9ca6b2420d0e4883d1de0 https://github.com/galaxyproject/galaxy/commit/a76960b9a6523376e8d9ca6b2420d... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- changed return statement to what it was before I forked. Commit: d5ea4ee380c5b8ed9a536e421c7365eeb379e3a2 https://github.com/galaxyproject/galaxy/commit/d5ea4ee380c5b8ed9a536e421c736... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/ui.less M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M static/maps/mvc/form/form-input.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-section.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/ui/ui-portlet.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/form/form-input.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-section.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/ui/ui-portlet.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css M test/qunit/test-data/fakeserver.js M test/qunit/tests/form_tests.js Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: a9b4d9518d1a7a7660d95a8dd312adae6ce48257 https://github.com/galaxyproject/galaxy/commit/a9b4d9518d1a7a7660d95a8dd312a... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- re-worked logic to be more clear that there are three different modes when handling name conflicts Commit: 607d10275169f54f54c6e4a9357a4bf5d05b946e https://github.com/galaxyproject/galaxy/commit/607d10275169f54f54c6e4a9357a4... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-12 (Fri, 12 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- changes based on flake8 erros Commit: d64d278ca9c3cc766620d1f3b0659dc8a6614e9a https://github.com/galaxyproject/galaxy/commit/d64d278ca9c3cc766620d1f3b0659... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-22 (Mon, 22 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- Add the ability to change the suffix template to 3 different preset values. Same as Flatten collection tool. Added a test to ensure that its working. Commit: 424acd5fcf0937b09a7be8c58e674d143d0402a8 https://github.com/galaxyproject/galaxy/commit/424acd5fcf0937b09a7be8c58e674... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-24 (Wed, 24 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- fixed flake formatting errors Commit: c29f481dceeaaa790be1d8fdadfd58f1cb2d68c6 https://github.com/galaxyproject/galaxy/commit/c29f481dceeaaa790be1d8fdadfd5... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py A lib/galaxy/tools/append_collection.xml Log Message: ----------- initial version of append collection tool. Allow's user to add one or more datasets to an existing collection. Provides options when we have name conflicts Commit: b97ddd7ea52da1215c8251029f632cc972c6dba3 https://github.com/galaxyproject/galaxy/commit/b97ddd7ea52da1215c8251029f632... 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test/qunit/tests/form_tests.js M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into collection_tools Commit: 5159f878cfbdaa2627be76db1d69741b3579b68f https://github.com/galaxyproject/galaxy/commit/5159f878cfbdaa2627be76db1d697... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-26 (Fri, 26 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- change tool description Commit: f88e8a19fa270615bdfe482ca4f2d1175f56d10b https://github.com/galaxyproject/galaxy/commit/f88e8a19fa270615bdfe482ca4f2d... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/append_collection.xml Log Message: ----------- changed tool name and description Commit: f54bf1bb3b0afc28d948a511001895abcaf8b15f https://github.com/galaxyproject/galaxy/commit/f54bf1bb3b0afc28d948a51100189... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml Log Message: ----------- Now allow filter_failed_collection to accept and filter out list:paired collection Commit: 97ba98037992a577a9a1a6b844893f63a7339034 https://github.com/galaxyproject/galaxy/commit/97ba98037992a577a9a1a6b844893... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- now change to see if the element has dataset_instance before attempting to call it. Commit: 4729565dfdc32482b177e3e2740f8abcbc23ab0f https://github.com/galaxyproject/galaxy/commit/4729565dfdc32482b177e3e2740f8... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-29 (Mon, 29 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- added AppendCollectionTool to list of tool_classes Commit: 19a09e18a84a860d60e66517b3b68b58628843c7 https://github.com/galaxyproject/galaxy/commit/19a09e18a84a860d60e66517b3b68... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py R lib/galaxy/tools/append_collection.xml Log Message: ----------- removed append_collection tool due to John request. MergeCollection should cover all cases that append would have anyway. Commit: ecc415369ff50dce02f5db73bdaf6fe8e60b6020 https://github.com/galaxyproject/galaxy/commit/ecc415369ff50dce02f5db73bdaf6... Author: takadonet <philipmabon@gmail.com> Date: 2016-08-30 (Tue, 30 Aug 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- added support to merge two list:paired collection together. Added single test to reflect new changes. Commit: 15ad14e6620706d6dbb39176783e274e01eebb3b https://github.com/galaxyproject/galaxy/commit/15ad14e6620706d6dbb39176783e2... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Enhance merge collection work from @Takadonet with more merge conflict actions. And allow it to work over any number of input collections. Commit: 448a27a4a1ebe2b25b40eca11b7aa319f7345c61 https://github.com/galaxyproject/galaxy/commit/448a27a4a1ebe2b25b40eca11b7aa... 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tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into collection_tools Commit: 49eac93882226e6f29624c676d593ae78719d7e5 https://github.com/galaxyproject/galaxy/commit/49eac93882226e6f29624c676d593... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-16 (Sun, 16 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/merge_collection.xml Log Message: ----------- Cleanup merge collection and get test cases working again. Commit: 7d938e2a23ca3ce8e3fac430bce494ce8f5238c3 https://github.com/galaxyproject/galaxy/commit/7d938e2a23ca3ce8e3fac430bce49... 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tools/metag_tools/shrimp_color_wrapper.py M tools/metag_tools/shrimp_wrapper.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/phenotype_association/pagetag.py M tools/phenotype_association/senatag.py M tools/solid_tools/maq_cs_wrapper.py M tools/solid_tools/solid_qual_stats.py M tools/sr_assembly/velvetg_wrapper.py M tools/sr_mapping/bfast_wrapper.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from jmchilton/collection_tools Enhance the Merge Collections Tool Commit: 31cb477e1a538c74360f039dda23907d0856adb6 https://github.com/galaxyproject/galaxy/commit/31cb477e1a538c74360f039dda239... Author: John Chilton <jmchilton@gmail.com> Date: 2016-10-17 (Mon, 17 Oct 2016) Changed paths: M config/tool_conf.xml.sample M lib/galaxy/tools/__init__.py M lib/galaxy/tools/filter_failed_collection.xml A lib/galaxy/tools/merge_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #2771 from Takadonet/dev Collection Operator tools Compare: https://github.com/galaxyproject/galaxy/compare/a895c823daaf...31cb477e1a53