Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e5505fa4de90cdb23f9fb1e00dcb4af6289521c https://github.com/galaxyproject/galaxy/commit/3e5505fa4de90cdb23f9fb1e00dcb... Author: Iyad Kandalaft ik@iyadk.com Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml A lib/galaxy/datatypes/mothur.py
Log Message: ----------- initial files by IyadKandalaft
Commit: f8a2dbd05a87782f5f0c30540ef463330d040589 https://github.com/galaxyproject/galaxy/commit/f8a2dbd05a87782f5f0c30540ef46... Author: shiltemann zazkia@gmail.com Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
Log Message: ----------- add mothur prefix
Commit: 8961d8bd3d52cdd1abeba6060a226192277dbc2d https://github.com/galaxyproject/galaxy/commit/8961d8bd3d52cdd1abeba6060a226... Author: shiltemann zazkia@gmail.com Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- use 'with open' throughout
Commit: 4311a4fbf84c073fbe01806ce7968c10cabfd00b https://github.com/galaxyproject/galaxy/commit/4311a4fbf84c073fbe01806ce7968... Author: shiltemann zazkia@gmail.com Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- minor changes to list creations
Commit: 65dde43041b94fd7f04f47369cb3302514a3e997 https://github.com/galaxyproject/galaxy/commit/65dde43041b94fd7f04f47369cb33... Author: shiltemann zazkia@gmail.com Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample
Log Message: ----------- remove sniffers for datatypes that were subclassed
Commit: 45bf09dad0c8b3db9c0f9973d9347932d108e172 https://github.com/galaxyproject/galaxy/commit/45bf09dad0c8b3db9c0f9973d9347... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/mothur.py
Log Message: ----------- add mothur prefix to extension, update sniffers and sniffer order, subclass taxonomy datatypes
Commit: ef32ee15fd9ee7a61c018a7e22a3cae0cc498b87 https://github.com/galaxyproject/galaxy/commit/ef32ee15fd9ee7a61c018a7e22a3c... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/mothur.py
Log Message: ----------- remove phylip datatype (not specific to mothur)
Commit: 6ac7ec56032e25e9f883421d5aba6d1e6165e2cc https://github.com/galaxyproject/galaxy/commit/6ac7ec56032e25e9f883421d5aba6... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- make sniffers for otu and distmatrices stricter
Commit: c43235011bf211da96b4507b986850ccc59567f8 https://github.com/galaxyproject/galaxy/commit/c43235011bf211da96b4507b98685... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- remove two unused classes
Commit: b833d385056f23dfb314e4c8162982374766e73d https://github.com/galaxyproject/galaxy/commit/b833d385056f23dfb314e4c816298... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
Log Message: ----------- stop using deprecated 'interpreter'
Commit: f3820538d186a1143443e47e764ad8ddc001d27f https://github.com/galaxyproject/galaxy/commit/f3820538d186a1143443e47e764ad... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- stylefixes
Commit: 31129e9d18b52eb9842a0ebbfe1eabbaedc73334 https://github.com/galaxyproject/galaxy/commit/31129e9d18b52eb9842a0ebbfe1ea... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths: M config/datatypes_conf.xml.sample
Log Message: ----------- subclass mothur.align
Commit: 43f7564365ac101bfd43c55b741b1543eed6457d https://github.com/galaxyproject/galaxy/commit/43f7564365ac101bfd43c55b741b1... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
Log Message: ----------- update sniffers and add doctests
Commit: a82a5b20ddd71e1a5180a15220e9aa000f307dbe https://github.com/galaxyproject/galaxy/commit/a82a5b20ddd71e1a5180a15220e9a... Author: shiltemann s.hiltemann@erasmusmc.nl Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/mothur.py
Log Message: ----------- stylefixes and updates set_metas
Commit: 3a74c774095c2d3967bba869e74cceaf94479f66 https://github.com/galaxyproject/galaxy/commit/3a74c774095c2d3967bba869e74cc... Author: shiltemann zazkia@gmail.com Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths: M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py M lib/galaxy/datatypes/mothur.py
Log Message: ----------- add python optimisations
Commit: f56e81a996511869f4a068418ffcd104c1b0ccdc https://github.com/galaxyproject/galaxy/commit/f56e81a996511869f4a068418ffcd... Author: shiltemann zazkia@gmail.com Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- allow for comment lines in Otu files
Commit: d47f8f577e358b4e7a71b15a905040e5d3b079d4 https://github.com/galaxyproject/galaxy/commit/d47f8f577e358b4e7a71b15a90504... Author: John Chilton jmchilton@gmail.com Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py
Log Message: ----------- Fixup exception handling in mothur datatypes.
Commit: d73a86d3658ed2ff7815ba5bd57ae63e527d4381 https://github.com/galaxyproject/galaxy/commit/d73a86d3658ed2ff7815ba5bd57ae... Author: John Chilton jmchilton@gmail.com Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths: M lib/galaxy/datatypes/sniff.py
Log Message: ----------- Add a sample sniff test for new Mothur datatype.
The existing sniffer tests with the mothur stuff tests the sniffers in isolation - this is more of an integration test that tests the sample datatype configuration for the newly added mothur stuff.
Commit: 04476160aa19f3ce5cbd345cd8b3073575ed327b https://github.com/galaxyproject/galaxy/commit/04476160aa19f3ce5cbd345cd8b30... Author: Saskia Hiltemann shiltemann@users.noreply.github.com Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths: M lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py
Log Message: ----------- Merge pull request #1 from jmchilton/mothur_datatypes
Small tweaks to mothur dataytpes.
Commit: c72381c528a9ab0afc231f1d109c8f4e66860b2e https://github.com/galaxyproject/galaxy/commit/c72381c528a9ab0afc231f1d109c8... Author: John Chilton jmchilton@gmail.com Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml A lib/galaxy/datatypes/mothur.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
Log Message: ----------- Merge pull request #2038 from shiltemann/mothur_datatypes
Import mothur datatypes
Compare: https://github.com/galaxyproject/galaxy/compare/a7bcd69f9e6b...c72381c528a9