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... Author: takadonet philipmabon@gmail.com Date: 2016-08-26 (Fri, 26 Aug 2016)

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config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js M 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lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/toolbox/watcher.py M lib/galaxy/util/__init__.py A lib/galaxy/util/postfork.py M lib/galaxy/util/template.py M lib/galaxy/web/framework/base.py A lib/galaxy/web/framework/middleware/batch.py M lib/galaxy/web/framework/middleware/sentry.py M lib/galaxy/web/proxy/__init__.py M lib/galaxy/web/proxy/js/lib/main.js M lib/galaxy/web/proxy/js/lib/proxy.js M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/config.py M lib/galaxy/webapps/tool_shed/controllers/hg.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M lib/tool_shed/galaxy_install/update_repository_manager.py M run.sh M scripts/bootstrap_history.py M scripts/common_startup.sh M static/maps/mvc/dataset/data.js.map M static/maps/mvc/form/form-data.js.map M static/maps/mvc/form/form-repeat.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-color-picker.js.map M static/maps/mvc/ui/ui-tabs.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/data.js M static/scripts/mvc/form/form-data.js M static/scripts/mvc/form/form-repeat.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-tabs.js M static/scripts/utils/utils.js M static/style/blue/base.css M static/style/blue/library.css M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/index.mako A test/api/test_api_batch.py M test/base/interactor.py A test/casperjs/api-batch-tests.js A test/functional/tools/dbkey_output_action.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/tool_provided_metadata_1.xml A test/functional/tools/tool_provided_metadata_2.xml A test/functional/tools/tool_provided_metadata_3.xml M test/qunit/test-data/fakeserver.js M 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... Author: John Chilton jmchilton@gmail.com Date: 2016-10-16 (Sun, 16 Oct 2016)

Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js A client/galaxy/scripts/libs/bbi/bigwig.js A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js A client/galaxy/scripts/libs/bbi/jszlib.js A client/galaxy/scripts/libs/bbi/spans.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form-workflow.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/tool/tools.js M client/galaxy/scripts/mvc/ui/ui-modal.js M client/galaxy/scripts/mvc/ui/ui-portlet.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/utils/utils.js A 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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... Author: Philip Mabon philipmabon@gmail.com Date: 2016-10-17 (Mon, 17 Oct 2016)

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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