 dcnorris
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3bc8bd3dca
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converted tabs to spaces
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2014-04-14 16:43:49 -04:00 |
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dcnorris
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e5201f8632
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adding support for the visualization of gtf file format in IGB
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2014-04-14 10:05:03 -04:00 |
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dcnorris
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1d5286610c
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Added IGB display support for bed graph files
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2014-04-10 09:48:59 -04:00 |
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Nicola Soranzo
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2ae82eda3d
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Use new Bcf class.
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2014-03-27 17:19:39 +01:00 |
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Aysam Guerler
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934db851e7
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Datatypes: Add datatype description to xml, Upload: Load description from xml
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2014-02-15 00:06:32 -05:00 |
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Carl Eberhard
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c4a740eded
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Graph datatypes: re-add to conf.sample returning False from all sniffers; the user must now manually change the type
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2013-10-17 13:14:11 -04:00 |
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Nate Coraor
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6a99bac16a
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Temporarily remove graph datatypes (necessary to avoid autodetection problems) until their sniffers are fixed. See also: a60d756aeb5d
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2013-10-10 10:42:56 -04:00 |
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Carl Eberhard
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1e2ea5e11c
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Datatypes: temporarily remove graph datatype sniffers (f3a985005267) until they can be made more discriminating
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2013-08-28 11:22:27 -07:00 |
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Carl Eberhard
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2687382a18
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Pull request #168 from Kyle Ellrott: add graph content datatypes SIF, XGMML, RDF
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2013-08-07 18:07:46 -04:00 |
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Jeremy Goecks
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92a7d07d00
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Add interval-to-bigwig converter, which creates a bigwig of coverage data for an interval dataset.
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2013-05-14 14:56:09 -04:00 |
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Jeremy Goecks
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4f3acda1ca
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Visualization framework: replace summary_tree with bigwig datatype for all feature track coverage data, yielding better performance and a standardized approach for working with coverage data. Update Trackster to work with bigwig coverage data.
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2013-05-09 11:44:45 -04:00 |
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Jeremy Goecks
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9003a86a37
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Use tabix rather than interval index for pileup data indexing.
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2013-04-20 10:06:26 -04:00 |
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Jeremy Goecks
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fb691bb29d
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Add pileup to interval_index converter.
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2013-04-16 17:45:52 -04:00 |
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Nicola Soranzo
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b6d79019ad
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Add generic ASN.1 text and binary datatypes
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2013-03-06 12:39:04 +01:00 |
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Daniel Blankenberg
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1c9861eca2
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First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.
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2013-02-14 15:13:06 -05:00 |
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Daniel Blankenberg
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a273960126
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Backout 3189a1bf18af
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2013-02-04 06:43:35 -05:00 |
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Daniel Blankenberg
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bab984ed69
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Add sentry_dsn to Tool Shed config.py' lib/galaxy/webapps/community/config.py
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2013-02-04 06:33:19 -05:00 |
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James Taylor
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15d72a247e
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genetrack: missed one reference to display application
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2013-02-03 23:39:06 -05:00 |
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James Taylor
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a4318d4817
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genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility
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2013-02-03 23:21:17 -05:00 |
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Jeremy Goecks
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189abc32d5
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Converter enhancements: (a) add bam to bigwig converter; (b) update datatypes.conf.sample to include new converter (disabled by default and documented with requirements) and remove unneeded dependency for bam to summary tree converter; and (c) remove deprecated page tags from bedgraph to bigwig converter.
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2012-12-07 10:33:39 -05:00 |
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Jeremy Goecks
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ec3eae321a
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Add chromatin interaction datatype to datatypes.conf, fix bug in data chrint data provider, and enable diagonal heat map track.
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2012-10-22 13:19:09 -04:00 |
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Jeremy Goecks
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015a1cd675
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Refactor PhyloViz components to work in new visualization framework and add sniffers for datatypes.
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2012-10-04 09:11:04 -04:00 |
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James Taylor
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2a2003c606
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circster: Allow data_standalone types to work; phyloviz: add tree datatypes to sample conf
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2012-09-10 17:09:09 -04:00 |
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Jeremy Goecks
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0d2a7cf7ea
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Add feature search to Trackster; typing in location box will search tracks in visualization for features that start with entered text. Works with both GFF/GTF and BED datasets. Fixes #611
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2012-09-05 17:26:43 -04:00 |
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Jeremy Goecks
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9f4e004786
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Update datatypes conf sample to include bedgraph to bigwig converter.
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2012-08-22 22:54:54 -04:00 |
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Daniel Blankenberg
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85c985db82
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Remove blastxml from datatypes_conf.xml.sample.
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2012-08-21 16:05:55 -04:00 |
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Jeremy Goecks
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9fabf5dfbe
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Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.
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2012-08-16 16:32:00 -04:00 |
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Ross Lazarus
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51e71a325c
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Adding a new datatype to datatypes_conf.xml.sample - toolshed compatible gzips created by a new automated
script wrapper.
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2012-06-06 12:08:55 +10:00 |
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Jeremy Goecks
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b261bc7335
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Do not use tabix for GFF/GTF because tabix is woefully naive about these data formats.
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2012-05-15 10:17:44 -04:00 |
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Jeremy Goecks
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50791f5802
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Use tabix for indexing and getting data from GTF files. This is faster and more flexible than using interval index.
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2012-04-23 09:08:29 -04:00 |
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Hiral Vora
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16753d3dbc
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Modifying datatypes_conf.xml.sample to include IGB files.
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2012-04-20 08:59:26 -04:00 |
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Daniel Blankenberg
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e344a49e48
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Allow BCF files to be uploaded.
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2012-04-17 09:47:25 -04:00 |
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Greg Von Kuster
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152f539560
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Eliminate duplicate galaxy.datatypes.images:Xpm sniffer entry from datatypes_conf.xml.sample.
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2012-04-16 13:09:06 -04:00 |
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Nate Coraor
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cc2385220f
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Miller Lab's Genome Diversity tools moved to the Tool Shed.
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2012-04-09 13:13:44 -04:00 |
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Greg Von Kuster
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8c9dd68f1f
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Eliminate the emboss 5 datatypes from datatypes_conf.xml.sample
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2012-03-21 16:47:58 -04:00 |
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Daniel Blankenberg
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9e6f192608
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Fix missing gatk_report datatype in datatypes_conf.xml.sample.
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2012-02-29 10:27:49 -05:00 |
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Jeremy Goecks
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e5e5cebe6b
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Enable visualization of ENCODE peak tracks. Create 'encodepeak' datatype and add data providers for new datatype.
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2012-02-23 12:23:36 -05:00 |
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Jeremy Goecks
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f926c93b5b
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Enable interval files to be converted to tabix.
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2012-02-22 15:23:44 -05:00 |
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Jeremy Goecks
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f13eb27286
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Enable interval files to be converted to interval_index and summary_tree datatypes.
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2012-02-22 13:57:17 -05:00 |
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Daniel Blankenberg
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11fd8d08e4
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Add RViewer external display application.
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2012-02-17 10:00:42 -05:00 |
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Daniel Blankenberg
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a25dbe5603
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GATK: add newly introduced gatkreport datatype, currently used by variant eval.
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2012-01-27 10:46:58 -05:00 |
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Nate Coraor
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943ce1de96
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Merged in jdlogicman/galaxy-central-add-xml-mimetype (pull request #16)
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2012-01-23 14:34:38 -05:00 |
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Greg Von Kuster
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651f0a7024
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Eliminate all references and support for datatype indexers since they have never been used - datatype converters do the same thing.
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2012-01-06 15:43:35 -05:00 |
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Daniel Blankenberg
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08013f4ef1
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Add UCSC VCF external display application.
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2011-12-20 15:40:07 -05:00 |
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Daniel Blankenberg
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cc38aae783
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Add Picard Interval List to BED6 converter.
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2011-12-16 14:39:40 -05:00 |
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Jeremy Goecks
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2c68904b30
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Add automatic conversions for SAM to BAM and SAM to summary tree. Enable SAM datasets to be visualized in Trackster.
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2011-12-06 09:34:19 -05:00 |
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Daniel Blankenberg
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8986dc2c81
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Add SAMTools mpileup.
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2011-11-21 16:30:34 -05:00 |
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Daniel Blankenberg
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09bcf6e95a
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Add VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).
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2011-11-15 17:24:38 -05:00 |
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Daniel Blankenberg
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0f98fc6814
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Add 'type_extension' attribute to datatypes_conf.xml that allows creating a datatype from an earlier declared datatype by referencing extension. Make several datatypes that had been direct instantiations from Data become subclasses of Binary.
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2011-11-15 14:28:08 -05:00 |
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John Duddy
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39f5a3995d
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Add support for generic XML files for tool integrations
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2011-10-31 17:16:17 -07:00 |
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