Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc8... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba760... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30bf.... This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c3... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d5... Author: Nate Coraor <nate@bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95e... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcafb... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/acb4cdf5843a...711070dc4c18 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.