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103 Commits
Author SHA1 Message Date
Nate Coraor e75f2b0895 Symlink sample configs back to config/ 2019-07-08 10:20:01 +02:00
Nate Coraor 42cf61fd36 Move some things from scripts/ to lib/ and some sample configs to 
lib/galaxy/config/sample/
 2016-07-07 13:49:27 -04:00
Devon Ryan 3d6c55d1ce Update the sample datatype_conf.xml file for bigwigs in IGV 2016-06-25 20:16:06 -04:00
Björn Grüning 11cdc4703a display TIFF in upload 2016-06-20 11:24:24 +02:00
Björn Grüning 30fd1d679b Merge pull request #2429 from shiltemann/mothur_datatypes 
small updates to Mothur datatypes
 2016-06-03 10:58:12 +02:00
shiltemann 110f0fe23d add mothur.tre datatype (subclass) 2016-05-23 16:46:10 +02:00
John Chilton c72381c528 Merge pull request #2038 from shiltemann/mothur_datatypes 
Import mothur datatypes
 2016-04-27 10:56:11 -04:00
Nicola Soranzo a85d6d5566 Merge pull request #1968 from jmchilton/csv_fix 
Improve tabular datatypes.
 2016-04-07 16:48:32 +01:00
John Chilton 0029949ed2 More fixups for specialized, more correct tabular datatypes. 
Followed through with @nsoranzo's comment:

1. overwrite CSV.sniff() and CSV.set_meta() methods with the ones from BaseCSV
2. remove BaseCSV class and rename CSV to BaseCSV
3. rename ExcelCSV class to CSV

Also renamed ExcelTSV to TSV and corrected another bug in sample datatypes noticed by @nsoranzo.
 2016-04-07 09:04:49 -04:00
Daniel Blankenberg 55074c8f33 Add Phinch as an external display application. Currently linking to a personal copy of Phinch, since it requires https://github.com/PitchInteractiveInc/Phinch/pull/54 2016-04-01 15:38:53 -04:00
shiltemann 31129e9d18 subclass mothur.align 2016-03-31 14:42:55 +02:00
shiltemann ef32ee15fd remove phylip datatype (not specific to mothur) 2016-03-30 14:37:05 +02:00
shiltemann 45bf09dad0 add mothur prefix to extension, update sniffers and sniffer order, subclass taxonomy datatypes 2016-03-30 14:19:44 +02:00
Bjoern Gruening 991e069ef2 enable obfs datatype during upload 2016-03-29 09:05:34 +02:00
shiltemann 65dde43041 remove sniffers for datatypes that were subclassed 2016-03-26 13:15:14 +01:00
shiltemann f8a2dbd05a add mothur prefix 2016-03-26 13:13:33 +01:00
Iyad Kandalaft 3e5505fa4d initial files by IyadKandalaft 2016-03-26 13:13:07 +01:00
John Chilton 5eb96a5fcf Merge PR #1156 into dev and fix #1818. 2016-03-21 14:05:54 +00:00
Bjoern Gruening 1e9b0e6dbd add molecule datatypes, like PDB and some cheminformatic ones 2016-03-20 18:06:14 +01:00
Daniel Blankenberg 0c57453c96 Add vcf.iobio as a display application. 2016-03-15 12:57:47 -04:00
Daniel Blankenberg 46728c5728 Add bam.iobio as a display application. 2016-03-15 12:56:54 -04:00
John Chilton 7e0427b8b7 Merge remote-tracking branch 'jmchilton/dev' into csv_fix 2016-03-01 07:32:44 +00:00
Remi Marenco c8469b7d0e Refactor the Html Datatype Class into text.py instead of images.py 2016-02-18 13:01:07 -05:00
John Chilton e106609c1c Add a more correct zip file type. 2016-02-03 13:33:04 +00:00
Gildas Le Corguillé 87f3ee48b0 add a zip datatype which won't be extracted 2016-02-03 16:46:50 +01:00
Björn Grüning 016fd38e72 Merge pull request #1148 from markiskander/bcfgz_to_bcf_converter 
Bcf.gz to bcf (and reverse) converters + bcf_bgzip data type
 2016-01-06 11:48:33 +01:00
John Chilton 7a960b0852 Small tweaks to CSV fixes by @Christian-B. 
- Update sample datatype conf.
 - Use Python naming conventions and PEP-8 style fixes.
 2016-01-04 13:42:10 +00:00
John Chilton a570956612 Merge pull request #396 from jessevdam/dev 
Added better support for formats that store triples.
 2015-12-03 15:25:13 -05:00
chambm 97415de3ce Move idpDB and MzSQlite formats from proteomics.py to binary.py, because the SQLite sniffer lives there, and more specialized formats must be registered for sniffing before the generic format 
Add proper idpDB sniffing logic (akin to MzSQlite) and test case
Add H5 sniffing based on magic number and test case
Add SQLite/IdpDB/MzSQlite/GeminiSQLite and H5 to default datatypes in registry.py
 2015-12-02 18:27:33 -06:00
Nate Coraor 9e28f2e786 Merge branch 'release_15.10' into dev 2015-11-30 14:13:26 -05:00
Greg Von Kuster 6fdff2d2f8 Add Strand-specific Coordinate Count datatype entry to the datatypes config. 2015-11-28 14:32:12 -05:00
Mark Iskander 825a20ef81 Modified more names, added bcf_bgzip to datatypes, added converters going both ways 2015-11-20 13:49:04 -06:00
John Chilton e4e44be27b Merge pull request #1004 from jj-umn/uniprotxml_datatype 
UniProtXML datatype
 2015-11-18 13:47:27 -05:00
John Chilton ee2b34c387 Merge pull request #950 from fescudie/dev 
Add BIOM v1 in default datatypes.
 2015-11-18 13:41:02 -05:00
youri d40d384a86 CRAM format 2015-11-16 22:57:02 +01:00
Jim Johnson 2a7bba5aba Add UniProtXML sniffer tag 2015-11-02 12:09:18 -06:00
Jim Johnson bafb8a9a4d Add uniprotxml datatype 2015-10-29 13:45:40 -05:00
fescudie fe0f9ba905 Add BIOM v1 in default datatypes. 2015-10-20 09:27:09 +02:00
Jim Johnson c869dde1e0 Fix typo. 2015-10-14 14:18:25 -05:00
Jim Johnson dde91947ac Add SearchGuiArchive datatype to binary 2015-10-14 11:46:58 -05:00
Greg Von Kuster 4657ce6f34 Add support for constructive solid geometry datatypes ply and vtk. 2015-10-13 11:22:50 -04:00
guerler 08f1e7b3ad Add pdf datatype to list of uploadable files 2015-10-12 18:04:47 -04:00
Michael R. Crusoe 383e9e0181 OxliLabelSet->OxliGraphLabels even in the config 2015-09-13 14:21:33 -07:00
Michael R. Crusoe 4064d0c598 add Oxli datatypes 2015-09-13 14:21:33 -07:00
Jesse c j van Dam fb2784003d Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 
Conflicts:
	.ci/pep8_sources.txt
	lib/galaxy/datatypes/graph.py
 2015-08-24 15:43:27 +02:00
Dannon Baker 19d9145594 One more bump to be the last tabular type detected, since ConnectivityTable is more specific. 2015-08-06 17:19:12 -04:00
Dannon Baker d270ccd078 Fix sniff order with respect to CSV interpreting SAM files as valid CSV prior to SAM sniffing. Test with 1.sam. 2015-08-06 14:58:06 -04:00
Carl Eberhard b1be4c1450 Datatypes: allow display_in_upload for h5 files 2015-07-16 10:35:12 -04:00
Dannon Baker 9b0ee0589a Resolve sample merge conflict. 2015-07-08 12:30:39 +01:00
youri 534d7b8b50 Added datatype definition for ConnectivityTable (*.ct) - RNA 2D structure file format 2015-07-07 17:30:54 +02:00