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
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
Jim Johnson
ab4dc39a67
Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite
...
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
...
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
Jesse c j van Dam
aea04a9871
Added better support for formats that store triples, these formats include 'N-Triples', 'N3','Turtle','RDF/XML' and 'JSON-LD'
2015-06-24 12:56:08 +02:00
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.
...
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
...
Conflicts:
config/datatypes_conf.xml.sample
2015-06-14 17:17:55 -04:00
John Chilton
508194f223
Fix sample datatype definition for CSV.
...
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.
...
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.
...
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
...
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
John Chilton