September 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1f53c3: Add missing tabular_to_dbnsfp.py for dbnsfp.tabula...
by GitHub 20 Sep '16

20 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_db… Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Commit: 7627abb3856a4e757b5ed5c55ec05a4f97bd4cac https://github.com/galaxyproject/galaxy/commit/7627abb3856a4e757b5ed5c55ec0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/c497ea534897...7627abb3856a

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[galaxyproject/galaxy] 1f53c3: Add missing tabular_to_dbnsfp.py for dbnsfp.tabula...
by GitHub 20 Sep '16

20 Sep '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 1f53c32ad68235537d8f6c843d1cd81eda5c11c3 https://github.com/galaxyproject/galaxy/commit/1f53c32ad68235537d8f6c843d1c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion This should have been added in https://bitbucket.org/galaxy/galaxy-central/pull-requests/640/ Actual source code comes from https://github.com/galaxyproject/tools-iuc/blob/master/datatypes/snpsift_db… Commit: b748250193a26ddce4010759b9a22d012d281b81 https://github.com/galaxyproject/galaxy/commit/b748250193a26ddce4010759b9a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-20 (Tue, 20 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py Log Message: ----------- Merge pull request #2938 from nsoranzo/release_16.04_tabular_to_dbnsfp [16.04] Add missing tabular_to_dbnsfp.py for dbnsfp.tabular to snpsiftdbnsfp conversion Compare: https://github.com/galaxyproject/galaxy/compare/b50d07d5bf12...b748250193a2

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[galaxyproject/usegalaxy-playbook] 3d4f12: Additional stuff for Bridges
by GitHub 19 Sep '16

19 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3d4f123bccb9b1ec1b1e089bbd718c76534f8704 https://github.com/galaxyproject/usegalaxy-playbook/commit/3d4f123bccb9b1ec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: M stage/host_vars/br005.bridges.psc.edu.yml A stage/secret_host_vars/br005.bridges.psc.edu.yml R stage/secret_host_vars/greenfield.psc.xsede.org.yml Log Message: ----------- Additional stuff for Bridges

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[galaxyproject/usegalaxy-playbook] a282f3: Update for Bridges
by GitHub 19 Sep '16

19 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a282f3acba310a95b317ed7b06c30d634c0059c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/a282f3acba310a95… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-19 (Mon, 19 Sep 2016) Changed paths: A stage/host_vars/br005.bridges.psc.edu.yml R stage/host_vars/greenfield.psc.xsede.org.yml M stage/inventory Log Message: ----------- Update for Bridges

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[galaxyproject/galaxy] bbf72e: CI testing of newly integrated tool schema (XSD).
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bbf72ef932f7e7ef314b905e17b4958180f4eb11 https://github.com/galaxyproject/galaxy/commit/bbf72ef932f7e7ef314b905e17b4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: A .ci/validate_test_tools.sh M .travis.yml R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M tox.ini Log Message: ----------- CI testing of newly integrated tool schema (XSD). - Add CI script that lints the XSD definition and then validates all test tools against it. - Add tox environment to run the aforementioned script. - Add Travis check through tox to run the script. - Drop the multi_page.xml test tool - pages have been removed from the framework and are not part of the schema (xref https://github.com/galaxyproject/galaxy/issues/1776) This will hopefully ensure that all new tool features get added to the schema (as long as there is a test tool for the feature). xref https://github.com/galaxyproject/galaxy/pull/2923 https://github.com/galaxyproject/galaxy/pull/2903 Largely based on work done in Galaxy-XSD by JeanFred (e.g. https://github.com/galaxyproject/Galaxy-XSD/commit/386ba087881877093d4be1f6…) Commit: 05ae9959078a94da25a16ed8ef13f2a2d6aceb45 https://github.com/galaxyproject/galaxy/commit/05ae9959078a94da25a16ed8ef13… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .ci/validate_test_tools.sh A scripts/validate_tools.sh Log Message: ----------- Refactor most of tool validation for CI into a standalone script. Commit: 8ca517dc8b937e5f435e2a5046e3ecc32c27d504 https://github.com/galaxyproject/galaxy/commit/8ca517dc8b937e5f435e2a5046e3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .travis.yml M tox.ini Log Message: ----------- More fixes pointed out by @nsoranzo for validation CI. Commit: a58d50e14f31c0639069959ef4d68b75ef331580 https://github.com/galaxyproject/galaxy/commit/a58d50e14f31c0639069959ef4d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M .travis.yml Log Message: ----------- Another fix thanks to @nsoranzo. Commit: 71cea6604d43c5fe6215f5656462ba6c1af69bb6 https://github.com/galaxyproject/galaxy/commit/71cea6604d43c5fe6215f5656462… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: A .ci/validate_test_tools.sh M .travis.yml A scripts/validate_tools.sh R test/functional/tools/multi_page.xml M test/functional/tools/samples_tool_conf.xml M tox.ini Log Message: ----------- Merge pull request #2932 from jmchilton/validate_test_tools CI testing of newly integrated tool schema (XSD). Compare: https://github.com/galaxyproject/galaxy/compare/f12723dc8311...71cea6604d43

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[galaxyproject/galaxy] 7e8bee: Deleting directories from SVN that should have bee...
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7e8bee8830d5d82e222b350d4bc240d1206e5af3 https://github.com/galaxyproject/galaxy/commit/7e8bee8830d5d82e222b350d4bc2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A galaxy.xsd Log Message: ----------- Deleting directories from SVN that should have been ignored. git-svn-id: https://svn.msi.umn.edu/tint/trunk@427 29e1c259-b37a-0410-ae23-5fb2df606144 Commit: 39fb238e666bb404b140b9ec37f1caeeb8a2637f https://github.com/galaxyproject/galaxy/commit/39fb238e666bb404b140b9ec37f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Work on galaxy support, implemented repeat blocks in the UI. Commit: a718608e838f796bddb159b4e303194db52b3085 https://github.com/galaxyproject/galaxy/commit/a718608e838f796bddb159b4e303… Author: Jean-Frédéric <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A README.md Log Message: ----------- Add basic ReadMe Commit: 6e689fa77eef72020f62e00149bddfae825e299f https://github.com/galaxyproject/galaxy/commit/6e689fa77eef72020f62e00149bd… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove custom namespaces Commit: e1fc626fc1d6f2e49519784bea217ea3022d4073 https://github.com/galaxyproject/galaxy/commit/e1fc626fc1d6f2e49519784bea21… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Change tool element to <xs:all> Element order is not enforced by Galaxy. Commit: 025a22b0e7bbb8f9fc89dac33c8e18fdfc49b36f https://github.com/galaxyproject/galaxy/commit/025a22b0e7bbb8f9fc89dac33c8e… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <requirements> tag set This includes: -<requirements> -<requirement> -Enumeration RequirementType Commit: 08f1faad44fde20cf0748d7c12785300d67942ec https://github.com/galaxyproject/galaxy/commit/08f1faad44fde20cf0748d7c1278… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Complete <repeat> tag set Add attributes min and max to Repeat element Commit: 9a9ba49caab8c63cff05153948160acccd80f912 https://github.com/galaxyproject/galaxy/commit/9a9ba49caab8c63cff0515394816… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <options> tag to <param> The <param> tag can contain <options> to dynamically create a list of options. Commit: 6b828d2b29b1612c82bcd7348625318628712aaf https://github.com/galaxyproject/galaxy/commit/6b828d2b29b1612c82bcd7348625… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <label> tag to <param> Commit: 150939e16a242a992d69bb771a6bf87f1936be40 https://github.com/galaxyproject/galaxy/commit/150939e16a242a992d69bb771a6b… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add missing attributes to <param> tag Add seven missing attributes to <param> tag Add the necessary datatypes for display, hierarchy and checked. Commit: 62c32df6f1d7de93f04cd3a9b5fd7572f91f4363 https://github.com/galaxyproject/galaxy/commit/62c32df6f1d7de93f04cd3a9b5fd… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add missing attributes and element to <data> tag Add three missing attributes to <data> tag Add <filter> element to sequence Commit: 73edfd6cf03c4366d4fd1036aa6fe3760958cd2a https://github.com/galaxyproject/galaxy/commit/73edfd6cf03c4366d4fd1036aa6f… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix indentation Commit: 91a166b7f5f42ee60495da20443b73d4bda1a502 https://github.com/galaxyproject/galaxy/commit/91a166b7f5f42ee60495da20443b… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <parallelism> tag Add the <parallelism> tag (which serves for splitting job) and the datatype for the 'method' attribute. Commit: f9c5cf28ef2f60867a81dd8b6da3454e46d2936a https://github.com/galaxyproject/galaxy/commit/f9c5cf28ef2f60867a81dd8b6da3… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <stdio> tag set to <tool> Add <stdio> tag set, to handle tool messages on standard output and standard error. - Add <stdio> tag - Add <regex> and <exit_code> sub elements - Add datatypes for 'range', 'level' and 'source' attributes Commit: 6e1d7e40a333d717a7c877c18eb94048dd99a7f0 https://github.com/galaxyproject/galaxy/commit/6e1d7e40a333d717a7c877c18eb9… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Change type for requirement version Version information can be too complex for xs:decimal (eg "0.12.7"). Change for xs:string. Commit: 642e88857caa09d968f4e5c740dc44475a64e288 https://github.com/galaxyproject/galaxy/commit/642e88857caa09d968f4e5c740dc… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add column, filter and validator tags Commit: 1787f1e89b4a311d9bae2c60effc851347da50e2 https://github.com/galaxyproject/galaxy/commit/1787f1e89b4a311d9bae2c60effc… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add ftype attribute to param tag in tests Commit: 6181d24704fd23b3370a961ba3fb573d0100f099 https://github.com/galaxyproject/galaxy/commit/6181d24704fd23b3370a961ba3fb… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <code> tag set Commit: 0da4d3c85361954a82fb8a0aa4c0f6bd742b9033 https://github.com/galaxyproject/galaxy/commit/0da4d3c85361954a82fb8a0aa4c0… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove required use from <requirement> version Commit: 8164cfd3ba691dbb11fc5f623610b726ad5f2b85 https://github.com/galaxyproject/galaxy/commit/8164cfd3ba691dbb11fc5f623610… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Edit <options> tag set Commit: bb285e4caee908cf4be30f0bf19ae21ffba20ebe https://github.com/galaxyproject/galaxy/commit/bb285e4caee908cf4be30f0bf19a… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <validator> to <param> Commit: 02aa90c4a477bb595540914df08ef9402275d84d https://github.com/galaxyproject/galaxy/commit/02aa90c4a477bb595540914df08e… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add 'split' attribute to <validator> Commit: e200148feef9ff553820272d7893b387e6e4723d https://github.com/galaxyproject/galaxy/commit/e200148feef9ff553820272d7893… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <actions> tag set Commit: 1c9513d6cb64315e742eab7befec7536dee766c8 https://github.com/galaxyproject/galaxy/commit/1c9513d6cb64315e742eab7befec… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Extend CheckedType to accept unspecified values According to the documentation, CheckedType can either be 'yes', 'true' or 'on' ; but many tools use '[Ff]alse' which seems to be accepted/ignored by Galaxy. Commit: b35b9fd52c78a891555660d7512e617b03d36cc0 https://github.com/galaxyproject/galaxy/commit/b35b9fd52c78a891555660d7512e… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add PermissiveBoolean datatype <xs:boolean> can either be 'true', 'false', '1' or 'O' ; but many Galaxy tools use 'True' and 'False' (capitalized), which appears to be ignored/accepted by Galaxy. This PermissiveBoolean type is meant to be used in place of xs:boolean when needed. Commit: dd0ba4293dc03db422a7b33e974c3b7554c287e9 https://github.com/galaxyproject/galaxy/commit/dd0ba4293dc03db422a7b33e974c… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add attributes 'ftype' and 'sort' to test <output> These are undocumented attributes. Commit: 4578e0a0f957ef7f851257b7bb605764712c5a44 https://github.com/galaxyproject/galaxy/commit/4578e0a0f957ef7f851257b7bb60… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <filter> Add attributes 'compare', 'keep' and 'value' to <filter> tag (though these attributes are not documented). Add CompareType for possible 'compare' values. Commit: 4bdfd455c58d00c5a28fdf1e6fc80d70648cb57a https://github.com/galaxyproject/galaxy/commit/4bdfd455c58d00c5a28fdf1e6fc8… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Edit filter tag for output tag Commit: 566e279172c98e417c7fca9cf04bda2e3abd2da5 https://github.com/galaxyproject/galaxy/commit/566e279172c98e417c7fca9cf04b… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Rewrite <actions> handling Commit: 1cda2e4439f28229d000f30120ecf69709606b6f https://github.com/galaxyproject/galaxy/commit/1cda2e4439f28229d000f30120ec… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'dbkey' attribute to TestParam Commit: 081c39e55161e1d1babebed1d159f2415a8e0adb https://github.com/galaxyproject/galaxy/commit/081c39e55161e1d1babebed1d159… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add 'from_file' value to ActionsOptionType Commit: b466de7e0a5e019d1a4264f2982f8c2012715241 https://github.com/galaxyproject/galaxy/commit/b466de7e0a5e019d1a4264f2982f… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Use PermissiveBoolean for ParamOption 'selected' Commit: 92b1076261ee0403ff8fb6f8e2601ba5149e9807 https://github.com/galaxyproject/galaxy/commit/92b1076261ee0403ff8fb6f8e260… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add attributes tool_type and URL_method to <tool> And corresponding enumeration Datatypes. Commit: e8f236a52e5c4081ef9a228e15ffefb50185db7f https://github.com/galaxyproject/galaxy/commit/e8f236a52e5c4081ef9a228e15ff… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- use PermissiveBoolean on two attributes of <param> Commit: 7d7b5a8d3dfc604335626f0abf806377dc2b630c https://github.com/galaxyproject/galaxy/commit/7d7b5a8d3dfc604335626f0abf80… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) value 'no' to CheckedType Commit: e19f1fb99a982cedebc74a3b42f0c376e19d46bc https://github.com/galaxyproject/galaxy/commit/e19f1fb99a982cedebc74a3b42f0… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) <uihints> to <tool> See /lib/galaxy/tools/__init__.py:1069 for usage Commit: 836aff4b3f70d6073bbd5f4d78d4b6688aed7baa https://github.com/galaxyproject/galaxy/commit/836aff4b3f70d6073bbd5f4d78d4… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <inputs> Add attributes 'action', 'check_values', 'method' and 'target' to <inputs>. Add relevant Target datatype. Commit: c4769e701302625031db4a7730e572b32c019ead https://github.com/galaxyproject/galaxy/commit/c4769e701302625031db4a7730e5… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add <sanitizer> tag Commit: 5419b1a4bce60a4459b59711acbf9c2652d5722d https://github.com/galaxyproject/galaxy/commit/5419b1a4bce60a4459b59711acbf… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attribute metadata_name to <param> Commit: 79cf1c57d8b6a1add066bf61ec18936bf1a8f6ee https://github.com/galaxyproject/galaxy/commit/79cf1c57d8b6a1add066bf61ec18… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attributes to <options> Add 'options_filter_attribute' attribute (see lib/galaxy/tools/parameters/basic.py) Add 'transform_lines' attribute (see lib/galaxy/tools/parameters/dynamic_options.py) transform_lines and Commit: 11b013f402b90c742789df87b6810e156a173171 https://github.com/galaxyproject/galaxy/commit/11b013f402b90c742789df87b681… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'ref_attribute' to <filter> Add attribute 'ref_attribute' to <filter> (see lib/galaxy/tools/parameters/dynamic_options.py:153) Commit: 65903327fa21536d44822ef94a9e75b2d29cf11d https://github.com/galaxyproject/galaxy/commit/65903327fa21536d44822ef94a9e… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) 'startswith' to <options> Add attribute 'startswith' to <options> tag (see lib/galaxy/tools/parameters/dynamic_options.py:416) Commit: d12766e260ea8d1e6ebe61806cb7e2b3eb55b886 https://github.com/galaxyproject/galaxy/commit/d12766e260ea8d1e6ebe61806cb7… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add (undocumented) attribute 'display' to <inputs> See lib/galaxy/tools/__init__.py:1531 Commit: 091b3b85687eeb8ef5becdf30ff81211b12f6f45 https://github.com/galaxyproject/galaxy/commit/091b3b85687eeb8ef5becdf30ff8… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix value baseurl in <param> 'type' attribute Commit: 395780d3d143982204c1f9ccf188df1deff51d55 https://github.com/galaxyproject/galaxy/commit/395780d3d143982204c1f9ccf188… Author: JeanFred <jean-frederic.berthelot(a)lifl.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix type of min and max in <validator> Commit: 2fdf2267b841d2701db424f9d2f458d8fbc2309b https://github.com/galaxyproject/galaxy/commit/2fdf2267b841d2701db424f9d2f4… Author: Pierre Lindenbaum <plindenbaum(a)yahoo.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A .gitignore A Makefile M README.md A citation.xsd A citations.xsd A galaxy.jxb M galaxy.xsd A test.urls Log Message: ----------- added doc and JXB bindings Commit: 2cecbe1922a9b5d75f34d42bedcd025a83fbae09 https://github.com/galaxyproject/galaxy/commit/2cecbe1922a9b5d75f34d42bedcd… Author: Pierre Lindenbaum <plindenbaum(a)yahoo.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- updated README Commit: f692d3a5ae244ce638be596723f369dade3ed501 https://github.com/galaxyproject/galaxy/commit/f692d3a5ae244ce638be596723f3… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A .travis.yml Log Message: ----------- Add Continuous integration with Travis for XSD linting At the very least these XSD files should be XML valid. Commit: cdbe79b4b657609724081c991466b0be13460d36 https://github.com/galaxyproject/galaxy/commit/cdbe79b4b657609724081c991466… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M .travis.yml Log Message: ----------- Fix dependency installation for Travis Build was failing with $ apt-get install libxml2-utils E: Could not open lock file /var/lib/dpkg/lock - open (13: Permission denied) E: Unable to lock the administration directory (/var/lib/dpkg/), are you root? APT dependencies must be installed as sudoer. Commit: 00a560ce1dbb093989b36f628abf08bf5ad3ee91 https://github.com/galaxyproject/galaxy/commit/00a560ce1dbb093989b36f628abf… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Add Travis badge to ReadMe Commit: 3315e9a8c424281df01e7521a9c9715447356059 https://github.com/galaxyproject/galaxy/commit/3315e9a8c424281df01e7521a9c9… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A test.sh Log Message: ----------- Add Shell test script Following the idea of @lindenb in the Makefile. This tests all the given URLs in test.urls and outputs a compliant TAP. Commit: bcc20e289fc9c4df1615530b264a6cada2e39974 https://github.com/galaxyproject/galaxy/commit/bcc20e289fc9c4df1615530b264a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Add me (@jmchilton) to authors list. My name is on the earliest commits (thanks for preserving that). Commit: 1b7f2a54f6c2b12d9340fe4c8c3e8de0f0f68afb https://github.com/galaxyproject/galaxy/commit/1b7f2a54f6c2b12d9340fe4c8c3e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M citation.xsd M test.urls Log Message: ----------- Fix CitationType attribute. Add Galaxy's test tool for citations to test.urls. Commit: 057c36997bd5c4c75a85acd5a9346f8c28eee015 https://github.com/galaxyproject/galaxy/commit/057c36997bd5c4c75a85acd5a934… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Update XSD for container tags. Add Galaxy test tool for Docker container tags to test.urls. Commit: bdf36556fbf4c4db4c343e51d6d78c1ac2030464 https://github.com/galaxyproject/galaxy/commit/bdf36556fbf4c4db4c343e51d6d7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Drop embeddedValue for test stuff. These were an extension to the Galaxy XML syntax for TINT - which is no longer actively maintained. Commit: f0799b5fbb9dfe54241b702c450f258c946bf326 https://github.com/galaxyproject/galaxy/commit/f0799b5fbb9dfe54241b702c450f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Start work on implementing assert_contents tag in tests. Just enough to get Galaxy's simple_contructrs.xml to validate - add this to test.urls. More work should be done on these - but it should be automated derived from Galaxy somehow. Commit: b479b7334fc6649606c5144da7c9225c82857e6b https://github.com/galaxyproject/galaxy/commit/b479b7334fc6649606c5144da7c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd M test.urls Log Message: ----------- Update XSD for very basic data collection usage. - Allow 'data_collection' parameters and allow them to specify a 'collection_type'. - Allow test parameters to be flat collections. - Add test/functional/tools/collection_paired_test.xml to test.urls to check all of this. Lots more TODO for recent tool collection support - output collections definitions, output collection tests, dynamic discovery tags, specifying nested collections for test inputs. Commit: 49f7d51f57eb2f72e01e37fdaf6c44ffe11898de https://github.com/galaxyproject/galaxy/commit/49f7d51f57eb2f72e01e37fdaf6c… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A LICENSE M README.md Log Message: ----------- Add MIT license Per agreement of all authors. Closes #2. Commit: 8947f29ef2596e750d2783206df547efc7ef40fd https://github.com/galaxyproject/galaxy/commit/8947f29ef2596e750d2783206df5… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M README.md Log Message: ----------- Expand history in ReadMe Commit: 5d40c7b3e2b66d91a52ae12cf48cda30d245d180 https://github.com/galaxyproject/galaxy/commit/5d40c7b3e2b66d91a52ae12cf48c… Author: Jean-Fred <JeanFred@github> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M LICENSE Log Message: ----------- Fix authors in License file Follow up on #2. Commit: a4e5568af7f206c61ebf7afd9165bd1e34181d0b https://github.com/galaxyproject/galaxy/commit/a4e5568af7f206c61ebf7afd9165… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- first try Commit: 8f8cc890bcfaceaf4870daa2d4e22e10018119c2 https://github.com/galaxyproject/galaxy/commit/8f8cc890bcfaceaf4870daa2d4e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Improvements to XSD: - Implement section. - Implement and document request_parameter_translation, request_parameter and its children (value_translation and append_param). - Implement detect_errors on the command block and document defaults. Commit: 63c019b13b44fedc9159909eb7995294d3653244 https://github.com/galaxyproject/galaxy/commit/63c019b13b44fedc9159909eb799… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Fix to previous commit. - Remove downstream config file type that was abandoned work and not in galaxy-core. - More documentation for configfile stuff. - Improvements to representation for output and santizer. Commit: 1125f1b8ea8b993ac5493f663b76c4ba54350ee4 https://github.com/galaxyproject/galaxy/commit/1125f1b8ea8b993ac5493f663b76… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Simplify schema and improve docs related to sanitization. Commit: 21cd752e252d17fdba2401cbe78bc3ef62ffd327 https://github.com/galaxyproject/galaxy/commit/21cd752e252d17fdba2401cbe78b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Improve docs on filter and change_format of outputs. Commit: 804c072d5af2e5704d57a503a84ad6733f03c1c0 https://github.com/galaxyproject/galaxy/commit/804c072d5af2e5704d57a503a84a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- And more progress... - Docs for help. - Docs for tests. - Docs for code files. - Implementing more of the assert_xxx test flags. - Improved coverage of test assertion element descriptions. Commit: 23449750d46e4df208fc46d1c2a4d3840cd080f4 https://github.com/galaxyproject/galaxy/commit/23449750d46e4df208fc46d1c2a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Refine test outputs and include syntax for testing extra files and md5sums. Commit: 3d3c3fee4f576408c223c723b57b003ae6ccf4c1 https://github.com/galaxyproject/galaxy/commit/3d3c3fee4f576408c223c723b57b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress. - Add strict to command. - Add conditional and repeat to test params. - Add count to output collections. - Implement more collection output attributes (type_source, etc...). - Reduce need for type on collection defs (since type_source can be defined). Commit: 80d086b861f1401568b967d96e2e37461ca677a2 https://github.com/galaxyproject/galaxy/commit/80d086b861f1401568b967d96e2e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Allow section in test parameters. - Implement basic metadata testing. Commit: 19b273cdf55df6b2593715d7daaf4690d8d6935b https://github.com/galaxyproject/galaxy/commit/19b273cdf55df6b2593715d7daaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Allow nested elements in test output collections (hackily) - Implement ``compare`` and ``delta`` for test output comparison. - Implement the new ``checksum`` output test. Commit: 7f5cc04c114bd5e696e7e54697e5a7bf58277fa7 https://github.com/galaxyproject/galaxy/commit/7f5cc04c114bd5e696e7e54697e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More progress... - Add tool action. - Stub workflow_compatible and profile_version attributes on tool. - Add many more attributes to parallelism tag. - Add maxseconds and expect_num_outputs to tool test tag. - Small fix to <repeat> block in test cases. - Implement assigning metadata in test params. - Allow more versitle ordering of test blocks (too permissive now). - Implement testing of output metadata and discovered datasets. - Add nginx_upload attribute used by upload.xml and various conditional attributes for pulling in values from Galaxy internals. - Implement the stub of a ``upload_dataset`` param and say not to use it. - Add color and library data parameter types. - More attributes to filters and validators. - Implement auto_format on outputs. - Implement filters and explicit data outputs on output collections. - Implement inputs as json element. - Add empty dataset validator. Commit: 49ff357854ff1a8dab9d792c0d97881f33c5a603 https://github.com/galaxyproject/galaxy/commit/49ff357854ff1a8dab9d792c0d97… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Stub out environment variables and add a new tool type. Commit: c6ae6ee8cb3c240923e4738f0e8f0a4a1134cbd5 https://github.com/galaxyproject/galaxy/commit/c6ae6ee8cb3c240923e4738f0e8f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R citation.xsd R citations.xsd M galaxy.xsd Log Message: ----------- Embed citations right in galaxy.xsd. Not that I mind splitting it up - but it will make a couple things easier downstream and those few tags weren't enough to warrent breaking things up like that. Commit: dcfdd3ceaa62ccee0a8d22c6d299eab2742df47f https://github.com/galaxyproject/galaxy/commit/dcfdd3ceaa62ccee0a8d22c6d299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Many more fixes derived from testing tools-iuc. Commit: 8c2a4e12758827b0855181de962ef0f0a61515a7 https://github.com/galaxyproject/galaxy/commit/8c2a4e12758827b0855181de962e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- And more progress - now covers all Galaxy test tools and all IUC. - Add <options> block. - Add <trackster_conf> block. - Add a newerish validator and allow filter/validator columns to be column names. - More permissives boolean values to match Galaxy in various places. - Other mostly obsecure features. Commit: ff6cca8635e6ce1c906dd316dcc0d6ab0bed7fb3 https://github.com/galaxyproject/galaxy/commit/ff6cca8635e6ce1c906dd316dcc0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Doc updates Commit: 491efe8c4951eedecc1635dbc972fb49ec883230 https://github.com/galaxyproject/galaxy/commit/491efe8c4951eedecc1635dbc972… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Doc improvements. Commit: 94ad78da97b98eee05a5ff0f890eec0e518845b7 https://github.com/galaxyproject/galaxy/commit/94ad78da97b98eee05a5ff0f890e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Much richer documentation for a few tags including ``command``. Commit: e9f08b411a0bf4ef8620bc66fb7c10d61112fb49 https://github.com/galaxyproject/galaxy/commit/e9f08b411a0bf4ef8620bc66fb7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More work on documentation - revise last commit and add repeats and sections. Commit: 2e31bc932dd9bd96d403cd8e6ef20715785c3eef https://github.com/galaxyproject/galaxy/commit/2e31bc932dd9bd96d403cd8e6ef2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Work on docs. Commit: 8f2f62a75a7aa256904821888c09682ebde99c83 https://github.com/galaxyproject/galaxy/commit/8f2f62a75a7aa256904821888c09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs... - Added docs for param's option. - Started work on validators and options, but are WIP though. Commit: 4bcfe568b713e9369d0d1e5090e140d7ebfee17c https://github.com/galaxyproject/galaxy/commit/4bcfe568b713e9369d0d1e5090e1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs for validators. Commit: 2980835dc7ec8b2ba2e1cde39142e0697c4fc9f8 https://github.com/galaxyproject/galaxy/commit/2980835dc7ec8b2ba2e1cde39142… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- A lot more documentation around parameter options. Also fixed a bit of a problem - turns out <filter> in action conditionals is very different than filter in options so I've split these types out. Commit: cd5328dce2aff381df95fa7b523dc40bc525f704 https://github.com/galaxyproject/galaxy/commit/cd5328dce2aff381df95fa7b523d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More documentation... Cleaned up the stdio tags and help section, flushed out citations and parameter options. Small touchups other places also. Commit: 24f46245e09ef044cca6804c48c994e49b70b69a https://github.com/galaxyproject/galaxy/commit/24f46245e09ef044cca6804c48c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Mention code files as a way to generate dynamic options. Transplant example from Galaxy wiki of doing this. Commit: 6481a00f88bff4bb7a7adbf2aaaee639e4649147 https://github.com/galaxyproject/galaxy/commit/6481a00f88bff4bb7a7adbf2aaae… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Flush out docs for requirements and child tags. Commit: 3af76de52ff56fca6b65d993ce91fb39c30af2d2 https://github.com/galaxyproject/galaxy/commit/3af76de52ff56fca6b65d993ce91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Flush out docs for sanitizers, configfiles, etc... Commit: b059c8b592b0f45dd669f8e9cbca714ed292ccac https://github.com/galaxyproject/galaxy/commit/b059c8b592b0f45dd669f8e9cbca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Working my way through basic parameter documentation. Commit: 366def7026a68e2bde75a140e3e4f1496966b1f2 https://github.com/galaxyproject/galaxy/commit/366def7026a68e2bde75a140e3e4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More work on parameters and environment variables. Commit: 4ba421e2f67de03dfa51ad8493f9a27beb159f27 https://github.com/galaxyproject/galaxy/commit/4ba421e2f67de03dfa51ad8493f9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Finishing first pass at filling out wiki docs for ``param``. And other small fixes. Commit: 5ad6e790e2f1a752beb748581469aa2e9f73477f https://github.com/galaxyproject/galaxy/commit/5ad6e790e2f1a752beb748581469… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Starting to polish and flush out data outputs documentation. Commit: e2d55ccf1685ec767d2c09715b189c7a1ff411cb https://github.com/galaxyproject/galaxy/commit/e2d55ccf1685ec767d2c09715b18… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- More docs - conditional output actions and some more on discover datasets. Commit: 89c8934727c7a8b8cc4ca7db10e7882d22542a87 https://github.com/galaxyproject/galaxy/commit/89c8934727c7a8b8cc4ca7db10e7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- A bunch of work on cleaning up and flushing out documentation for test tags. Commit: c607727d83c079a2859ed9026d26edbb52f4bcf9 https://github.com/galaxyproject/galaxy/commit/c607727d83c079a2859ed9026d26… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Document the test ``output_collection`` tag. Commit: fc440a87c4883a9244d5e45783e2f27b639319cb https://github.com/galaxyproject/galaxy/commit/fc440a87c4883a9244d5e45783e2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix missing annotation. Commit: 60def6204d1ba2299442a76856f19ab53ffe1e92 https://github.com/galaxyproject/galaxy/commit/60def6204d1ba2299442a76856f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fixes of structure broken with docs. Commit: b74c1a5b0baa6da94ca45f11a1e8e2057fcf2790 https://github.com/galaxyproject/galaxy/commit/b74c1a5b0baa6da94ca45f11a1e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Use the new action conditional filter. Commit: 195fd46604a64ad8928ead83d6cd6f7f51a2639c https://github.com/galaxyproject/galaxy/commit/195fd46604a64ad8928ead83d6cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Add a fictious XML schema with Galaxy stuff. New attributes: - deprecated - best_practices (provides links of the form http://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_…) Commit: 4dd8da09b8bd1917094622039adfe01cffa2fd40 https://github.com/galaxyproject/galaxy/commit/4dd8da09b8bd1917094622039adf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Remove embedded best practice stuff - the help will have links now. Commit: c4f03079d7fefb2e37790b4d07fe7d0a67990d8d https://github.com/galaxyproject/galaxy/commit/c4f03079d7fefb2e37790b4d07fe… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fill out some docs for test sections... Commit: 0c6be2095710fbb79bd9b9fdd231e960bb9f2ce8 https://github.com/galaxyproject/galaxy/commit/0c6be2095710fbb79bd9b9fdd231… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M test.sh Log Message: ----------- Revise automated testing, check against test tools and IUC tools. Commit: b9d25b848c333226e503d4f301187a43dbebc584 https://github.com/galaxyproject/galaxy/commit/b9d25b848c333226e503d4f30118… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Document testing discovered datasets and metadata. Commit: 8b7ae4bc7b446b0b00758f6cf0c98e7eaece96ce https://github.com/galaxyproject/galaxy/commit/8b7ae4bc7b446b0b00758f6cf0c9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Fix a syntax error. Commit: 236bdf5a40d0d720a72b7c71b03e2cb79fc576d4 https://github.com/galaxyproject/galaxy/commit/236bdf5a40d0d720a72b7c71b03e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M galaxy.xsd Log Message: ----------- Update the link for multiple outputs. Commit: 3d7ae4e38fea3d7f84368ccb57f107f0c13f9749 https://github.com/galaxyproject/galaxy/commit/3d7ae4e38fea3d7f84368ccb57f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R .gitignore R .travis.yml R LICENSE R Makefile R README.md R galaxy.jxb R galaxy.xsd A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/Makefile A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/tools/xsd/test.sh A lib/galaxy/tools/xsd/test.urls R test.sh R test.urls Log Message: ----------- Relocate Galaxy XSD files into Galaxy directory structure. Commit: 491c9fd519be37b6c6f57cd4082d981c9f411ba5 https://github.com/galaxyproject/galaxy/commit/491c9fd519be37b6c6f57cd4082d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: R lib/galaxy/tools/xsd/Makefile R lib/galaxy/tools/xsd/test.urls Log Message: ----------- Cleanup XSD for move to Galaxy core. Commit: c4d8dddc5cbfe416e5931e409db9e63804688f1e https://github.com/galaxyproject/galaxy/commit/c4d8dddc5cbfe416e5931e409db9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd A lib/galaxy/tools/xsd/test.sh Log Message: ----------- Merge branch 'master' of Galaxy-XSD into 'dev' Commit: babaf7a2c675648e2851f81d985a72321b4eeb44 https://github.com/galaxyproject/galaxy/commit/babaf7a2c675648e2851f81d985a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd R lib/galaxy/tools/xsd/test.sh Log Message: ----------- Address reviewer comments on XSD. - Merge in @bgruening's numerous awesome fixes. - Remove test script with issues that make if not a fit for this repo in that form (noted by @nsoranzo). - Incorporate other changes to the XSD suggested by @nsoranzo. Commit: 70251b5b6a8363a627fccf90f642c3a02cc57cd5 https://github.com/galaxyproject/galaxy/commit/70251b5b6a8363a627fccf90f642… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/tools/xsd/LICENSE Log Message: ----------- Update the LICENSE for the XSD file. Commit: 9d24d55cb5e515b8e8f9654e070ae17aae864367 https://github.com/galaxyproject/galaxy/commit/9d24d55cb5e515b8e8f9654e070a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Add XSD contributors to CONTRIBUTORS.md. Commit: f12723dc8311b35c9cf7271dc3bc46f640bde00b https://github.com/galaxyproject/galaxy/commit/f12723dc8311b35c9cf7271dc3bc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M CONTRIBUTORS.md A lib/galaxy/tools/xsd/LICENSE A lib/galaxy/tools/xsd/README.md A lib/galaxy/tools/xsd/galaxy.jxb A lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #2923 from jmchilton/merge_xsd_into_core Merge Galaxy-XSD into project Compare: https://github.com/galaxyproject/galaxy/compare/31b4eb155fa8...f12723dc8311

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[galaxyproject/galaxy] 7a8d9a: Catch failure to import grp in util (for Pulsar on...
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7a8d9af16b97677656234c68d88c760495b4d322 https://github.com/galaxyproject/galaxy/commit/7a8d9af16b97677656234c68d88c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Catch failure to import grp in util (for Pulsar on Windows) Commit: 31b4eb155fa8f9f9d13d17ed60592f9cd99f23db https://github.com/galaxyproject/galaxy/commit/31b4eb155fa8f9f9d13d17ed6059… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #2928 from natefoo/windows-util-fix Catch failure to import grp in util (for Pulsar on Windows) Compare: https://github.com/galaxyproject/galaxy/compare/4c60b8120304...31b4eb155fa8

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[galaxyproject/usegalaxy-playbook] efe2bd: Move Test's install database to SQLite in CVMFS
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: efe2bda16ea1b8af5f79b7daae10949cb1f6b441 https://github.com/galaxyproject/usegalaxy-playbook/commit/efe2bda16ea1b8af… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- Move Test's install database to SQLite in CVMFS

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[galaxyproject/galaxy] 8616c0: Log the resolved dependency type
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8616c0e87c055ed8e41563625498818a76769b2f https://github.com/galaxyproject/galaxy/commit/8616c0e87c055ed8e41563625498… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-09-13 (Tue, 13 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Log the resolved dependency type Commit: 646428d73f9cbcd312ed3ff5eff8e36ee12f213e https://github.com/galaxyproject/galaxy/commit/646428d73f9cbcd312ed3ff5eff8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove change handler for data and collection multiinput selectors in old run workflow form Commit: b399c086254f35d8536c1afa9fd7a2e50ec339a9 https://github.com/galaxyproject/galaxy/commit/b399c086254f35d8536c1afa9fd7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-14 (Wed, 14 Sep 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/__init__.py Log Message: ----------- Merge pull request #2918 from martenson/pick-dep-log [16.07] cherry pick logging the resolved dependency type Commit: 67a3cf34ca0e639791ac88e849d120dce355d3ef https://github.com/galaxyproject/galaxy/commit/67a3cf34ca0e639791ac88e849d1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #2920 from guerler/fix_collection_refresh [16.07] Prevent refresh for collection selector in old run workflow form Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066 https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d4… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: c497ea534897b4c1875186961e96da52129c4a3a https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 [16.07] Update python-ldap module Commit: 4c60b812030423f7e4c755f7cbc57c83083ea834 https://github.com/galaxyproject/galaxy/commit/4c60b812030423f7e4c755f7cbc5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/f34ab79d22b2...4c60b8120304

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[galaxyproject/galaxy] dc5aff: Update python-ldap module
by GitHub 16 Sep '16

16 Sep '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: dc5aff7e44e2b0f767b7578935d46db7d7707066 https://github.com/galaxyproject/galaxy/commit/dc5aff7e44e2b0f767b7578935d4… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-09-15 (Thu, 15 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: c497ea534897b4c1875186961e96da52129c4a3a https://github.com/galaxyproject/galaxy/commit/c497ea534897b4c1875186961e96… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-09-16 (Fri, 16 Sep 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2924 from nsoranzo/release_16.07_backport_2738 [16.07] Update python-ldap module Compare: https://github.com/galaxyproject/galaxy/compare/67a3cf34ca0e...c497ea534897

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