Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 17e82957af9d4a586ee8262f0fb6e98041d436f5 https://github.com/galaxyproject/galaxy/commit/17e82957af9d4a586ee8262f0fb6e... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- add edam_data infrastructure to the Galaxy datatypes Commit: 8a2b08096ad197df229df8f77eeeed2c4d3e5068 https://github.com/galaxyproject/galaxy/commit/8a2b08096ad197df229df8f77eeee... Author: Hervé Ménager <herve.menager@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- add basic EDAM data metadata for data.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 5714c85a79d88d4efddcc30f414d376be9a79306 https://github.com/galaxyproject/galaxy/commit/5714c85a79d88d4efddcc30f414d3... Author: Hervé Ménager <herve.menager@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- add basic EDAM data metadata for sequence.py datatypes Based on agreement with bgruening, jongithub, and fmareuil on the annotation of datatypes with EDAM data concepts. Commit: 98e33d0b525db1ce3d7a66e7ee2d8fb63798d366 https://github.com/galaxyproject/galaxy/commit/98e33d0b525db1ce3d7a66e7ee2d8... Author: Hervé Ménager <herve.menager@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py Log Message: ----------- add EDAM data/formats to assembly datatypes Commit: 4ebeb548fdea3d157b62cae7a6e613e7821e292d https://github.com/galaxyproject/galaxy/commit/4ebeb548fdea3d157b62cae7a6e61... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/xml.py Log Message: ----------- add EDAM format and data for Phylo XML Commit: 907950df803e881bbefc4bf16ad8e9a0cff5725d https://github.com/galaxyproject/galaxy/commit/907950df803e881bbefc4bf16ad8e... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/triples.py Log Message: ----------- complete EDAM annotations for triple datatypes. Commit: c0867c665306bc59d8353a3fb192f49c87bbd7d7 https://github.com/galaxyproject/galaxy/commit/c0867c665306bc59d8353a3fb192f... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/tracks.py Log Message: ----------- complete EDAM annotations for Gene track format Commit: 0002eac91fa644e22aa5b939405e6e4801239384 https://github.com/galaxyproject/galaxy/commit/0002eac91fa644e22aa5b939405e6... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- complete EDAM annotations in text datatypes. Commit: 425cee668d3d0ab2b0f4912aabb370b600218199 https://github.com/galaxyproject/galaxy/commit/425cee668d3d0ab2b0f4912aabb37... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/qualityscore.py Log Message: ----------- add EDAM annotations to quality datatypes. Commit: c69aa8b54923b2df4ad6b7a430459a6767fb8f27 https://github.com/galaxyproject/galaxy/commit/c69aa8b54923b2df4ad6b7a430459... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add EDAM annotation to proteomics datatypes Commit: 0511d72e4a14e8d0c357733564f1ad6cea649723 https://github.com/galaxyproject/galaxy/commit/0511d72e4a14e8d0c357733564f1a... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/msa.py Log Message: ----------- add EDAM annotations to msa datatypes. Commit: 2a7436eb630d79072b8f1c4a80ccf1262a195cef https://github.com/galaxyproject/galaxy/commit/2a7436eb630d79072b8f1c4a80ccf... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- add EDAM annotations to interval datatypes. Commit: ec7519b267229ae4c13c6687332d3bb6e467718b https://github.com/galaxyproject/galaxy/commit/ec7519b267229ae4c13c6687332d3... Author: Hervé Ménager <hmenager@pasteur.fr> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/images.py Log Message: ----------- add EDAM annotations to image datatypes. Commit: 6929cd4cd15e176054bec286c440ca7f97589efe https://github.com/galaxyproject/galaxy/commit/6929cd4cd15e176054bec286c440c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/text.py Log Message: ----------- Address review comments by @nsoranzo Commit: 50fe4914339ac6c1f2a80c87eb4ee89967db9297 https://github.com/galaxyproject/galaxy/commit/50fe4914339ac6c1f2a80c87eb4ee... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/datatypes.py Log Message: ----------- Fix PEP8 for biotools PR Commit: 2a5b04075cd3d3f467c58f2ef134088931725d6f https://github.com/galaxyproject/galaxy/commit/2a5b04075cd3d3f467c58f2ef1340... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/images.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Fix some review comments Commit: 9460e6ea4910d086409419b5e17a2ce34da0f15a https://github.com/galaxyproject/galaxy/commit/9460e6ea4910d086409419b5e17a2... Author: Nicola Soranzo <nicola.soranzo@tgac.ac.uk> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/xml.py Log Message: ----------- More constistent ordering. Remove some blank lines Commit: 1b7c4395e279903a13f61c0789dd868628fc943f https://github.com/galaxyproject/galaxy/commit/1b7c4395e279903a13f61c0789dd8... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2016-05-20 (Fri, 20 May 2016) Changed paths: M lib/galaxy/datatypes/assembly.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/images.py M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/msa.py M lib/galaxy/datatypes/proteomics.py M lib/galaxy/datatypes/qualityscore.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/text.py M lib/galaxy/datatypes/tracks.py M lib/galaxy/datatypes/triples.py M lib/galaxy/datatypes/xml.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parser/output_objects.py M lib/galaxy/webapps/galaxy/api/datatypes.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #2387 from nsoranzo/edam_data Add support for EDAM data annotations to datatypes Compare: https://github.com/galaxyproject/galaxy/compare/b6f8e1c7996c...1b7c4395e279