[galaxyproject/galaxy] fa3a23: WIP: add a SelectTagParameter
Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa3a2371e1b2873456a3034874036d9b8cadd01c https://github.com/galaxyproject/galaxy/commit/fa3a2371e1b2873456a3034874036... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py Log Message: ----------- WIP: add a SelectTagParameter Commit: 4afbdbab31791101578be08acc3526e04c1835d6 https://github.com/galaxyproject/galaxy/commit/4afbdbab31791101578be08acc352... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-04 (Sun, 04 Feb 2018) Changed paths: M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Fix unit tests Commit: 04b0cfcc1388de18aeb93a39fa44451009bbd67f https://github.com/galaxyproject/galaxy/commit/04b0cfcc1388de18aeb93a39fa444... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-07 (Wed, 07 Feb 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Make `get_datasets_for_group` case insensitive to tag Commit: 45b2b7f434fc1bd1e646c72c6024bacc482a8b8e https://github.com/galaxyproject/galaxy/commit/45b2b7f434fc1bd1e646c72c6024b... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M .ci/check_py3_compatibility.sh M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .gitignore M .travis.yml M CONTRIBUTING.md M Makefile M README.rst M client/.babelrc M client/GruntFile.js M client/README.md M client/bower.json A client/galaxy/docs/bootstrap.md A client/galaxy/docs/galaxy-buttons.md A client/galaxy/docs/galaxy-forms.md A client/galaxy/docs/galaxy-masthead.md A client/galaxy/docs/galaxy-menus.md A client/galaxy/docs/galaxy-messages.md A client/galaxy/docs/galaxy-panels.md A client/galaxy/docs/galaxy-tables.md A client/galaxy/docs/galaxy-tabs.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/apps/chart.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/apps/panels/tool-panel.js M 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test/unit/jobs/dynamic_tool_destination/ymltests.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_params.py M test/unit/managers/test_HistoryManager.py M test/unit/test_galaxy_mapping.py M test/unit/test_remote_shell.py A test/unit/test_rule_utils.py M test/unit/test_security_helper.py A test/unit/test_security_passwords.py M test/unit/tools/test_collect_primary_datasets.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_dataset_matcher.py M test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools/test_tool_dependency_description.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_tool_validation.py M test/unit/tools/test_toolbox.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/unittest_utils/tempfilecache.py M test/unit/visualizations/plugins/test_VisualizationPlugin.py M test/unit/visualizations/plugins/test_VisualizationsRegistry.py M test/unit/web/framework/test_webapp.py M test/unit/workflows/test_extract_summary.py M test/unit/workflows/test_modules.py A tool-data/intermine_simple_display.loc.sample A tools/data_source/intermine.xml M tools/data_source/upload.py M tools/data_source/upload.xml M tools/evolution/codingSnps.xml M tools/extract/extract_genomic_dna.xml M tools/extract/liftOver_wrapper.xml M tools/filters/bed_to_bigbed.xml M tools/filters/cutWrapper.pl M tools/filters/sorter.py M tools/filters/sorter.xml M tools/filters/wig_to_bigwig.xml M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_importer.xml M tools/genomespace/genomespace_push.xml M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml M tools/sr_mapping/bfast_wrapper.xml M tools/stats/filtering.py M tools/stats/filtering.xml M tox.ini Log Message: ----------- Merge remote-tracking branch 'jmchilton/dev' into select_tag_parameter Commit: d417e9b239309707274011d4199b8f827fcc0f6d https://github.com/galaxyproject/galaxy/commit/d417e9b239309707274011d4199b8... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-24 (Tue, 24 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Flush out collection tag parameters a bit. - Switch select_tag to group_tag as a parameter name - since it is restricted to group_tags and we don't call data parameters select_data. - Add minimal XSD documentation for this new parameter type. - Add example tools - for single and multiple tags. - Add API tests for these tools and the tag handling. Commit: e5c532298d5db34da04d8f046ebe44abddbbaa64 https://github.com/galaxyproject/galaxy/commit/e5c532298d5db34da04d8f046ebe4... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Make tag order stable when using group_tag parameters. Commit: 6677e7b91385d027989613bdc621108da76e8425 https://github.com/galaxyproject/galaxy/commit/6677e7b91385d027989613bdc6211... Author: John Chilton <jmchilton@gmail.com> Date: 2018-07-25 (Wed, 25 Jul 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix failing import/export test for group_tag changes. Commit: 5a914b9fa71ff2c00d7ba1a7c1dc3ccbb8437eae https://github.com/galaxyproject/galaxy/commit/5a914b9fa71ff2c00d7ba1a7c1dc3... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Keep all user-selected tags, including duplicates Commit: 95e8a3491280cc26d435bebc1cf03488d7db3b88 https://github.com/galaxyproject/galaxy/commit/95e8a3491280cc26d435bebc1cf03... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Correct copy-pasted docstring Commit: 55436c38008c3d1b261b7d9dfc728cc968bd6622 https://github.com/galaxyproject/galaxy/commit/55436c38008c3d1b261b7d9dfc728... Author: John Chilton <jmchilton@gmail.com> Date: 2018-08-07 (Tue, 07 Aug 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py A test/functional/tools/collection_cat_group_tag.xml A test/functional/tools/collection_cat_group_tag_multiple.xml M test/functional/tools/samples_tool_conf.xml M test/unit/test_objectstore.py M test/unit/tools/test_wrappers.py Log Message: ----------- Merge pull request #5457 from mvdbeek/select_tag_parameter Allow selecting subset of collection by group tag Compare: https://github.com/galaxyproject/galaxy/compare/d1423b6e18cb...55436c38008c **NOTE:** This service has 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.
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