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
Jim Johnson
ab4dc39a67
Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite
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This is a SQLite schema for representing Peptide Spectral Matches from mzid and mzML datatypes.
2015-07-05 04:33:39 -05:00
John Chilton
235f432c43
Merge pull request #366 from yhoogstrate/dev
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Datatype definition for Dot-Bracket notation (dbn)
2015-07-02 08:23:59 -05:00
Ira Cooke
089cd474d0
Change raw to thermo.raw
2015-06-27 08:42:45 +10:00
Ira Cooke
cca245c62c
Change RAW to ThermoRAW and add to sniffers
2015-06-26 06:24:18 +10:00
Ira Cooke
c2cf786e76
Remove trailing spaces on line 46
2015-06-25 09:06:42 +10:00
Ira Cooke
031b4e01c0
Back out trailing space removal
2015-06-25 09:06:02 +10:00
Ira Cooke
3593d9c45c
Remove trailing spaces
2015-06-24 09:10:14 +10:00
Ira Cooke
734a429d3c
Add Proteomics Sniffers above GenericXML
2015-06-23 10:00:03 +10:00
Ira Cooke
b16d224fce
Add proteomics datatypes
2015-06-23 09:33:27 +10:00
youri
486899c021
DotBracket datatype definition is in line with Datatype description at Galaxy wiki
2015-06-19 09:19:16 +02:00
y.hoogstrate@erasmusmc.nl
4e5338d24e
updates to DotBracket
2015-06-17 13:31:27 +02:00
y.hoogstrate@erasmusmc.nl
41e346adfe
Added support for DotBracket notation
2015-06-17 11:11:14 +02:00
John Chilton
19dbf2f780
Allow specifying EDAM format for dynamic subclass datatypes.
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Use this to specify the EDAM format for genbank.
2015-06-15 11:17:43 -04:00
John Chilton
bdf1738885
Merge remote-tracking branch 'jmchilton/dev' into HEAD
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Conflicts:
config/datatypes_conf.xml.sample
2015-06-14 17:17:55 -04:00
John Chilton
508194f223
Fix sample datatype definition for CSV.
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For me it seems like the viz plugins only detect the datatype if the plugin datatype (e.g. ``tabular.CSV``) is explicitly instantiated by some extension directly. In your sample config you have ``subclass="True"`` so ``tabular.CSV`` wasn't working. This is probably a bug with the datatype code - but nonetheless I think dropping subclass from the sample is an okay workaround - because it does seem to be a direct mapping.
2015-06-03 10:52:59 -04:00
John Chilton
884e824d72
Merge remote-tracking branch 'vavrusa/table-datatype' into dev.
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Conflicts:
lib/galaxy/datatypes/tabular.py
2015-06-03 10:52:42 -04:00
John Chilton
bb88dcb059
Make the data manager JSON datatype's class more specific.
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Use Json base class instead of text - fixes data manager type for PR #80 .
2015-05-22 10:20:48 -04:00
Eric Rasche
21368266ce
Implement XMFA Datatype
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This is used with Mauve/ProgressiveMauve.
Additionally a bug is fixed in the Stockholm datatype which
would have prevented proper sequence count autodetection.
2015-05-18 12:58:42 -05:00
Daniel Blankenberg
f52bbbf50e
Add display for Interval files at IGV via bedstrict.
2015-05-14 14:51:43 -04:00
Eric Rasche
a940f19e15
Merged down datatypes
2015-05-07 12:27:22 -05:00
Eric Rasche
148acf0ddc
Add RData and RData.gz formats
2015-05-07 11:59:01 -05:00
Eric Rasche
791785c1a5
Move stockholm as well
2015-05-06 09:56:41 -05:00
Eric Rasche
d1c1af3bff
Move ddatatypes upwards of images
2015-05-05 15:16:29 -05:00
Eric Rasche
ec363b2b39
Add in hmmer2 datatypes
2015-05-05 15:03:41 -05:00
Eric Rasche
c1840a46b5
Bump version of hmm format
2015-05-05 14:54:15 -05:00
Eric Rasche
7ef0d4e6eb
Move msa datatypes into separate file
2015-05-05 14:42:25 -05:00
Eric Rasche
eeecf4103c
Include hmmer3 text format
2015-05-05 14:30:41 -05:00
Marek Vavrusa
bc8bdadca8
datatypes: extracted TabularData superclass from Tabular, CSV subclass
2015-04-30 17:20:32 +02:00
Bjoern Gruening
ce74ed5dce
add emboss datatypes
2015-04-23 15:49:11 +02:00
Matt Shirley
f6299976f3
Checkout proper branch...
2015-04-06 15:01:04 -04:00
Daniel Blankenberg
74242d9f50
Add an External Display application for viewing gff/gtf files at IGV.
2015-04-02 10:57:05 -04:00
Nate Coraor
002fef995a
Fix a typo in datatypes_conf.xml.sample
2015-02-27 14:21:22 -05:00
John Chilton
b5533cfe0e
Merged in BjoernGruening/galaxy-central-1/compressed_upload (pull request #630 )
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Add CompressedArchive as datatype and do not uncomress it during upload.
2015-01-23 14:13:25 -05:00
John Chilton
2d227d2daf
Merged in BjoernGruening/galaxy-central-1/snpeff_datatype (pull request #640 )
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Add SnpEff datatypes
2015-01-23 12:12:43 -05:00
Bjoern Gruening
b0d92cadd7
Remove not needed datatype, we now can filter datatypes by metadata.
2015-01-17 14:05:44 +01:00
Bjoern Gruening
d1d03abd0e
add back RNADotPlotMatrix sniffing
2015-01-16 23:38:41 +01:00
Bjoern Gruening
503543e36b
merge
2015-01-16 23:30:05 +01:00
Bjoern Gruening
0f0364e9fa
activate SnpSiftDbNSFP and dbnsfp.tabular
2015-01-16 22:08:29 +01:00
Bjoern Gruening
b75445e64d
activate snpeffdb and snpeffdbv4
2015-01-16 21:42:08 +01:00
Dannon Baker
dc5f826c40
Merged in BjoernGruening/galaxy-central-1/rna_eps_format (pull request #625 )
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Add RNA dotplot matrix as datatype.
2015-01-12 16:55:10 -05:00
Bjoern Gruening
5b96f80b48
Add CompressedArchive as datatype and do not uncomress it during upload.
2015-01-12 22:36:20 +01:00
Daniel Blankenberg
b022e92f5b
Add gemini.sqlite datatype.
2015-01-09 14:48:56 -05:00
Bjoern Gruening
19705f29c3
add rna_eps filetype
2015-01-06 17:18:01 +01:00
John Chilton
02609845b1
Fix for Pull Request #614 .
2015-01-05 16:09:45 -05:00
Björn Grüning
656c04b77a
Activate arff datatype by default
2014-12-23 00:27:36 +00:00
Björn Grüning
cc3ee556ea
Add Arff datatype and sniffer to datatypes_conf.xml.
2014-12-16 12:16:00 +00:00
Bjoern Gruening
06107a9fa6
Add OWL & OBO datatype.
2014-10-27 16:13:14 +01:00
John Chilton
8be7544485
Add IPython Notebook and JSON datatypes
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Based on work from Bjoern and Eric. Made some modifications to ensure they do not attempt to read all of very large files and added a configuration option that must be enabled to use fancy notebook viewing.
To enable fancy notebooks one also needs to - `pip install jinja2 pygments ipython` into Galaxy's virtualenv.
2014-10-18 18:38:04 -04:00
Dannon Baker