- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8cee21: Fixes <param argument="--set" /> not working when ...
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8cee212708f4de75c4bf066ac1dec0752bea0a5d https://github.com/galaxyproject/galaxy/commit/8cee212708f4de75c4bf066ac1de… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fixes <param argument="--set" /> not working when help="" is not set Commit: 09911084f3b424d4822d4b5baed7fa3ca1a0a3b9 https://github.com/galaxyproject/galaxy/commit/09911084f3b424d4822d4b5baed7… Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js Log Message: ----------- Fixes <param argument="--set" /> not working when help="" is not set (indentation) Commit: d7dd9f9040be7a66e414322a67e15bea1b93a9f6 https://github.com/galaxyproject/galaxy/commit/d7dd9f9040be7a66e414322a67e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M static/maps/mvc/form/form-input.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/form/form-input.js Log Message: ----------- Rebuild client stuff for #1650. Commit: d93f095c7f56c85c871ef82f532c68e12d3a3318 https://github.com/galaxyproject/galaxy/commit/d93f095c7f56c85c871ef82f532c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-input.js M static/maps/mvc/form/form-input.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/form/form-input.js Log Message: ----------- Merge remote-tracking branch 'jmchilton/param_argument_fix' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/d97e8bbbbce8...d93f095c7f56

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[galaxyproject/galaxy] 9551fc: Add the `scientific` platform (Scientific Linux) a...
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9551fc07b475b4095b7d002315cbc05bdf0925b5 https://github.com/galaxyproject/galaxy/commit/9551fc07b475b4095b7d002315cb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL. Commit: 9ead68aeca6722f62d3d6fabae6484aa00246615 https://github.com/galaxyproject/galaxy/commit/9ead68aeca6722f62d3d6fabae64… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1669 from natefoo/scientificlinux-tag-compat [16.01] Add the `scientific` platform (Scientific Linux) as binary compatible with RHEL Compare: https://github.com/galaxyproject/galaxy/compare/bb95a65b2201...9ead68aeca67

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[galaxyproject/galaxy] 17a168: Warn on optional select test parameter.
by GitHub 04 Feb '16

04 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17a1683a383d7f375b77371548ff7d349a561a96 https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Warn on optional select test parameter. Commit: ccdb027d38428a38d79b4272fadb076b7f428825 https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Prevent optional test parameters in conditionals Commit: 6fa7f1e1edda25ec36f2373148af223493924803 https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam to new 0.8.4+gx1. Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #8 from jmchilton/fix_optional_001 Warn on optional select test parameter. Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details. Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16 Commit: 66f20e7df91074e07cbade57b20deb68cb840a55 https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix method signature of bam.set_meta to include a positional argument which is now required. Commit: d6325c5039f28062a2cf49d00c091d83a92865c3 https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Update data providers pysam.AlignmentFile usage Commit: a95827751f463f35c67e76f84127f850972244c5 https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1637 from guerler/fix_optional_001 [16.01] Prevent optional test parameters in conditionals Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7 https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- fix show_welcome_with_login = True Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Merge pull request #1664 from bgruening/release_16.01 fix `show_welcome_with_login = True` Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py M test-data/3.bam Log Message: ----------- Merge pull request #1638 from dannon/pysam_84_update Pysam 84 update [16.01] Commit: 246870c459cffd48a0fe7b4963e674638298e620 https://github.com/galaxyproject/galaxy/commit/246870c459cffd48a0fe7b4963e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge branch 'release_16.01' into dev Commit: d97e8bbbbce862eb6b4f8f5732cd0baa029e9e20 https://github.com/galaxyproject/galaxy/commit/d97e8bbbbce862eb6b4f8f5732cd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/tools/__init__.py M lib/galaxy/visualization/data_providers/genome.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js M test-data/3.bam Log Message: ----------- Merge pull request #1667 from natefoo/dev Merge release_16.01 to dev Compare: https://github.com/galaxyproject/galaxy/compare/b82efd937504...d97e8bbbbce8

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[galaxyproject/galaxy] bf989f: correct typo in text datatype
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bf989f6051303658c6bc537fc1e00c877c55c6e1 https://github.com/galaxyproject/galaxy/commit/bf989f6051303658c6bc537fc1e0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- correct typo in text datatype Commit: bb95a65b2201509ce950d6c3c578f8d417f83cc4 https://github.com/galaxyproject/galaxy/commit/bb95a65b2201509ce950d6c3c578… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- Merge pull request #1666 from martenson/correct-datatype-typo [16.01] correct typo in text datatype Compare: https://github.com/galaxyproject/galaxy/compare/2641f0af9ac8...bb95a65b2201

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[galaxyproject/galaxy] 04af1a: Always use the python hashlib for verifying the vi...
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6 https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always use the python hashlib for verifying the virtualenv download in common_startup.sh rather than attempting to use sha256sum. Older versions of coreutils (such as in RHEL 6) did not include the --strict argument to sha256sum. Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1668 from natefoo/venv-checksum [16.01] Always use the python hashlib method for verifying the virtualenv download Compare: https://github.com/galaxyproject/galaxy/compare/cd3f3b330db3...2641f0af9ac8

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[galaxyproject/galaxy] 6fa7f1: Bump pysam to new 0.8.4+gx1.
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 6fa7f1e1edda25ec36f2373148af223493924803 https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Bump pysam to new 0.8.4+gx1. Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details. Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M test-data/3.bam Log Message: ----------- More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16 Commit: 66f20e7df91074e07cbade57b20deb68cb840a55 https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix method signature of bam.set_meta to include a positional argument which is now required. Commit: d6325c5039f28062a2cf49d00c091d83a92865c3 https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c09… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Update data providers pysam.AlignmentFile usage Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/visualization/data_providers/genome.py M test-data/3.bam Log Message: ----------- Merge pull request #1638 from dannon/pysam_84_update Pysam 84 update [16.01] Compare: https://github.com/galaxyproject/galaxy/compare/b5d1c7721ee2...cd3f3b330db3

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[galaxyproject/usegalaxy-playbook] fdaac8: Update Main and datatypes_conf.xml
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fdaac8f0aedc2a56535b02399bd8bbc33a4cfbc1 https://github.com/galaxyproject/usegalaxy-playbook/commit/fdaac8f0aedc2a56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M production/group_vars/all.yml M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update Main and datatypes_conf.xml Commit: c5fd01dce4930436147c883e5bf98e4678530ae6 https://github.com/galaxyproject/usegalaxy-playbook/commit/c5fd01dce4930436… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Version changes in the IE cache. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/159171d8b706...…

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[galaxyproject/galaxy] 45f523: fix show_welcome_with_login = True
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7 https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8c… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- fix show_welcome_with_login = True Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/layout/page.js Log Message: ----------- Merge pull request #1664 from bgruening/release_16.01 fix `show_welcome_with_login = True` Compare: https://github.com/galaxyproject/galaxy/compare/a95827751f46...b5d1c7721ee2

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[galaxyproject/usegalaxy-playbook] 159171: Update Test
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 159171d8b706f10cf0451ac71e8871db4f090c28 https://github.com/galaxyproject/usegalaxy-playbook/commit/159171d8b706f10c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-03 (Wed, 03 Feb 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 17a168: Warn on optional select test parameter.
by GitHub 03 Feb '16

03 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 17a1683a383d7f375b77371548ff7d349a561a96 https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Warn on optional select test parameter. Commit: ccdb027d38428a38d79b4272fadb076b7f428825 https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Prevent optional test parameters in conditionals Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #8 from jmchilton/fix_optional_001 Warn on optional select test parameter. Commit: a95827751f463f35c67e76f84127f850972244c5 https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1637 from guerler/fix_optional_001 [16.01] Prevent optional test parameters in conditionals Compare: https://github.com/galaxyproject/galaxy/compare/39aff8457201...a95827751f46

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