- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] cd9db0: Provide ToolDataTableManager for backwards compati...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cd9db0bffa68cec4891f38db77af578757d3b63d https://github.com/galaxyproject/galaxy/commit/cd9db0bffa68cec4891f38db77af… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Provide ToolDataTableManager for backwards compatibility Broken in 7df9dce63d635d66a0a9ce5045135ab49b7ef506 Commit: 1b1962ea490cdf3f7ff97bfc0f570235ef8ad7fc https://github.com/galaxyproject/galaxy/commit/1b1962ea490cdf3f7ff97bfc0f57… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/tool_shed/tools/data_table_manager.py Log Message: ----------- Merge pull request #5924 from mvdbeek/fix_data_managers [18.01] Provide ToolDataTableManager for backwards compatibility Compare: https://github.com/galaxyproject/galaxy/compare/e68eaeecbf66...1b1962ea490c

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[galaxyproject/galaxy] 8d4666: Update version to 18.05.rc1
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 8d4666578d4dc2c0374ef105659d69931efa1f4e https://github.com/galaxyproject/galaxy/commit/8d4666578d4dc2c0374ef105659d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.rc1 Commit: dbb08fe7620610812189049481740215c12f9eb6 https://github.com/galaxyproject/galaxy/commit/dbb08fe762061081218904948174… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5980 from martenson/version-18.05 [18.05] Update version to 18.05.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/c41c84eec6e8...dbb08fe76206

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[galaxyproject/galaxy] 8d4666: Update version to 18.05.rc1
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d4666578d4dc2c0374ef105659d69931efa1f4e https://github.com/galaxyproject/galaxy/commit/8d4666578d4dc2c0374ef105659d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.05.rc1 Commit: 53e67733660a8061a31de1a2a867e46e35fa2465 https://github.com/galaxyproject/galaxy/commit/53e67733660a8061a31de1a2a867… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 18.09.dev Commit: 8b51c30aa7c1e7ea711e22f81a4156ea1bcda769 https://github.com/galaxyproject/galaxy/commit/8b51c30aa7c1e7ea711e22f81a41… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Log Message: ----------- Merge branch 'version-18.05' into version-18.09.dev Commit: 7580a28b39175c221525abf74c0438a89b59f13f https://github.com/galaxyproject/galaxy/commit/7580a28b39175c221525abf74c04… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #5982 from martenson/version-18.09.dev start Version 18.09.dev Compare: https://github.com/galaxyproject/galaxy/compare/c41c84eec6e8...7580a28b3917

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[galaxyproject/galaxy] e58034: Correct examples in dynamic job conf doc, remove h...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: c41c84eec6e8cfc6291dd85ce58ba4b34b394bb1 https://github.com/galaxyproject/galaxy/commit/c41c84eec6e8cfc6291dd85ce58b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c1e5fb829016...c41c84eec6e8

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[galaxyproject/galaxy] e58034: Correct examples in dynamic job conf doc, remove h...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Commit: c41c84eec6e8cfc6291dd85ce58ba4b34b394bb1 https://github.com/galaxyproject/galaxy/commit/c41c84eec6e8cfc6291dd85ce58b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/c1e5fb829016...c41c84eec6e8

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[galaxyproject/galaxy] e58034: Correct examples in dynamic job conf doc, remove h...
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: e58034b9876d4fb148049b9cc56a7a99473a7531 https://github.com/galaxyproject/galaxy/commit/e58034b9876d4fb148049b9cc56a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Correct examples in dynamic job conf doc, remove handlers section from basic sample job config (defining a single default handler is no longer needed). Fixes #5976. Commit: e68eaeecbf6641d48487b130988b012bcd2202ca https://github.com/galaxyproject/galaxy/commit/e68eaeecbf6641d48487b130988b… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M config/job_conf.xml.sample_basic M doc/source/admin/jobs.md Log Message: ----------- Merge pull request #5981 from natefoo/job-doc-fixes [18.01] Minor Job documentation corrections Compare: https://github.com/galaxyproject/galaxy/compare/20e9934bc592...e68eaeecbf66

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[galaxyproject/galaxy]
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] a5c75d: Correct access for FTP files in composite datatype
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a5c75d2f954f697497747412fd2a998fa61019b0 https://github.com/galaxyproject/galaxy/commit/a5c75d2f954f697497747412fd2a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Correct access for FTP files in composite datatype Commit: 3ab2afb5e5bd82b3aa89500b9c2f80913a054316 https://github.com/galaxyproject/galaxy/commit/3ab2afb5e5bd82b3aa89500b9c2f… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- backport move_merge fix from #5922 Commit: 88bf6bbdaa2d15355192eb3c9087151f7712209d https://github.com/galaxyproject/galaxy/commit/88bf6bbdaa2d15355192eb3c9087… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge pull request #5943 from erasche/fix-ftp-composite-upload [18.01] Correct access for FTP files in composite datatype Commit: 20e9934bc5922f8d20dd31540a4dce9086495832 https://github.com/galaxyproject/galaxy/commit/20e9934bc5922f8d20dd31540a4d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/data_manager/manager.py Log Message: ----------- Merge pull request #5958 from abretaud/movemerge1801 [18.01] Backport to 18.01 the move_merge fix from #5922 Commit: c1e5fb82901600bd109fba133bc0f7c62313b3ea https://github.com/galaxyproject/galaxy/commit/c1e5fb82901600bd109fba133bc0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1624b6ce7d38...c1e5fb829016

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[galaxyproject/galaxy] 251526: Add `version` attribute to tool requirements
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2515267ca5a058d2029c589357f518b1cfb372b8 https://github.com/galaxyproject/galaxy/commit/2515267ca5a058d2029c589357f5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml 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/wig_to_bigwig.xml Log Message: ----------- Add `version` attribute to tool requirements instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` . Follow-up on https://github.com/galaxyproject/galaxy/pull/5544 . See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for an explanation why that's preferrable for future-proof reproducibility. Also, small fixes to `tools/evolution/codingSnps.xml` . Commit: 1624b6ce7d382c5ad1a883a5ca7f86106460e96c https://github.com/galaxyproject/galaxy/commit/1624b6ce7d382c5ad1a883a5ca7f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/fasta_to_2bit.xml M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml 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/wig_to_bigwig.xml Log Message: ----------- Merge pull request #5973 from nsoranzo/followup_on_5544 Add `version` attribute to some tool requirements Compare: https://github.com/galaxyproject/galaxy/compare/e7158658d026...1624b6ce7d38

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[galaxyproject/galaxy] d9904b: Fix for split columns rule definition.
by GitHub 25 Apr '18

25 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9904bf595c3815c4827bb0852004d036600936e https://github.com/galaxyproject/galaxy/commit/d9904bf595c3815c4827bb085200… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Fix for split columns rule definition. Commit: 8af243c176fd9c261277327750aaa71806add4ef https://github.com/galaxyproject/galaxy/commit/8af243c176fd9c261277327750aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js 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-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py Log Message: ----------- Allow rule based operations on existing collections. Allow the rules DSL & GUI component to operate on existing collections to allow filtering, sorting, modifying identifiers and general re-organization of existing collections (e.g. the outputs of tools). Implementing this as a collection operation tool so that it should be executable interactively in the tool form and in a batch fashion as part of workflow executions. For this to be tracked properly as a tool execution and to work properly in the tool form, I've implemented a new tool framework and tool form parameter type called "rules". This can thought of as a more GUI friendly alternative to my proposed collection operations that consumed JavaScript expressions. This includes API tests for both tool and workflow execution of the new tool as well as Selenium tests for tool form execution, workflow editor interactions, and workflow running. Commit: c225c5dbd651b048b3354e97a8821d8148b559fe https://github.com/galaxyproject/galaxy/commit/c225c5dbd651b048b3354e97a882… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Add simple help for apply rules tool. Commit: d2b8ad9105e5c06c8ab3685672c1a6dc64b31406 https://github.com/galaxyproject/galaxy/commit/d2b8ad9105e5c06c8ab3685672c1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- RuleBuilder tool param fix for to_dict. An exception in generating a "text representation" of a None value was preventing the rest of to_dict from running properly for that parameter value. This restores the rule preview table in the tool form. Commit: a6d052a6819d2bc277744b3e2633785c31c844fb https://github.com/galaxyproject/galaxy/commit/a6d052a6819d2bc277744b3e2633… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js Log Message: ----------- Fix modal title for apply_rules branch changes. Commit: 383eb0d2736269d24d595ed5b8aa730908812be3 https://github.com/galaxyproject/galaxy/commit/383eb0d2736269d24d595ed5b8aa… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M config/tool_conf.xml.sample Log Message: ----------- Add apply rules tool to standard tool xml sample Commit: f4eda4fd173b64d782a39da97d7a2b224a7637c3 https://github.com/galaxyproject/galaxy/commit/f4eda4fd173b64d782a39da97d7a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Fix up help language in apply_rules tool. Commit: cf2f6d7dcf2dba76dc02f1fe6ab0abd360584ef4 https://github.com/galaxyproject/galaxy/commit/cf2f6d7dcf2dba76dc02f1fe6ab0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py Log Message: ----------- Fix selenium tests failing because APPLY_RULES appears twice in panel. Commit: dbd86642d514badcc0fedf3f822f19d7b4dd9d15 https://github.com/galaxyproject/galaxy/commit/dbd86642d514badcc0fedf3f822f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-24 (Tue, 24 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/rules/rule-definitions.js Log Message: ----------- Merge other recent rule PRs into apply_rules branch. Commit: e7158658d026b7559adb173cea1ac0a26852bca8 https://github.com/galaxyproject/galaxy/commit/e7158658d026b7559adb173cea1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-25 (Wed, 25 Apr 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue A client/galaxy/scripts/components/RulesDisplay.vue M client/galaxy/scripts/mocha/tests/rules_tests.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js 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-view.js M client/galaxy/scripts/mvc/rules/rule-definitions.js M client/galaxy/scripts/mvc/tool/tool-form.js A client/galaxy/scripts/mvc/ui/ui-rules-edit.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/tool_conf.xml.main M config/tool_conf.xml.sample M lib/galaxy/app.py M lib/galaxy/dataset_collections/type_description.py M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py A lib/galaxy/tools/apply_rules.xml M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/tools/parser/xml.py A lib/galaxy/util/rules_dsl.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/rules_dsl_spec.yml A test/base/rules_test_data.py M test/base/workflow_fixtures.py M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml M test/selenium_tests/test_tool_form.py M test/selenium_tests/test_uploads.py M test/selenium_tests/test_workflow_editor.py M test/selenium_tests/test_workflow_run.py A test/unit/test_rule_utils.py M test/unit/tools/test_parsing.py Log Message: ----------- Merge pull request #5819 from jmchilton/apply_rules Allow rule based operations on existing collections. Compare: https://github.com/galaxyproject/galaxy/compare/8f8dc08a4cbe...e7158658d026

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