316 Commits

Include renames

Author	SHA1	Message	Date
Dave Bouvier	9b8e5dc885	Remove migrated tools from the tool conf files.	2014-05-19 13:02:11 -04:00
Dave Bouvier	83af05b1f2	Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.	2014-04-01 11:04:32 -04:00
Dave Bouvier	ba17a35a99	Remove stats/wiggle_to_simple, which is an exact duplicate of filters/wiggle_to_simple.	2014-02-14 12:34:58 -05:00
Nate Coraor	9c64fc123e	Remove broken and/or obsolete tools.	2014-01-27 13:58:31 -05:00
Dave Bouvier	448d9f55eb	Migrate 43 tools from the distribution to the tool shed.	2014-01-27 09:53:14 -05:00
Nate Coraor	cc0a59eb9e	merge stable.	2013-11-30 12:47:19 -05:00
Nate Coraor	e197bc6742	Remove broken GeneTrack tools.	2013-11-30 12:46:53 -05:00
Nate Coraor	fda2063db2	Remove broken indel analysis tools.	2013-11-11 12:11:54 -05:00
John Chilton	73206460d6	Backed out changeset 9532e80796ec	2013-11-07 13:02:22 -05:00
John Chilton	4a3820ef58	Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines. ... As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html). There are still two copies.	2013-11-07 12:56:48 -05:00
Daniel Blankenberg	57f2ef0844	One more occurance of fastq_to_fasta that was dropped.	2013-10-10 16:25:43 -04:00
Dave Bouvier	667efbd863	Restore the fastq_to_fasta that was not migrated.	2013-10-10 16:16:19 -04:00
Dave Bouvier	8937b1fc60	Remove migrated tools that were somehow restored to tool_conf.xml.sample	2013-10-10 16:12:52 -04:00
Ross Lazarus	8c4f96ed81	backout -r 10808	2013-10-08 10:55:24 +11:00
Ross Lazarus	7938d1fc81	local changes	2013-10-05 09:51:18 +10:00
Ross Lazarus	f2065f4a24	Starting the Rgenetics deprecation process - removing all rgenetics sections from tool_conf.xml.sample and fastqc update to dance around EBI_SRA download bogus file extensions	2013-05-30 14:57:13 +10:00
Daniel Blankenberg	a2a1a15b6f	Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).	2013-02-06 17:34:36 -05:00
Daniel Blankenberg	a422a9ed9f	Update Yogeshwar Kelkar's Microsatellite tools.	2013-01-11 09:48:47 -05:00
Dave Bouvier	917d5a72e8	Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.	2012-11-26 10:18:47 -05:00
Jeremy Goecks	9b25796399	eXpress in tool menus: (a) move to position after Cuff* tools and (b) add to main's tool conf.	2012-11-21 09:56:01 -05:00
Dave Bouvier	c968460662	Migrate Picard tools to the tool shed.	2012-10-24 11:09:20 -04:00
Dave Bouvier	c2eeee7b9f	Migrate BWA to the tool shed.	2012-09-28 15:35:44 -04:00
Dannon Baker	0b2e939d4d	Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.	2012-08-22 16:12:59 -04:00
Remi Marenco	65da5344a0	Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests	2012-07-23 14:17:23 -04:00
Remi Marenco	44701c866d	Merge ... Hg: changed lib/galaxy/datatypes/converters/sam_or_bam_to_summary_tree_converter.py	2012-07-18 10:48:59 -04:00
Remi Marenco	dd7f9dc3a7	eXpress tool wrapped in Galaxy. Added in "NGS: RNA Analysis".	2012-07-17 17:12:51 -04:00
Daniel Blankenberg	b2c152dbf8	Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed.	2012-07-10 17:35:30 -04:00
Daniel Blankenberg	e96a915591	Remove FreeBayes from tool_conf.xml.sample/main since it has been migrated to the toolshed.	2012-07-10 17:20:55 -04:00
Daniel Blankenberg	e8fe4c4dc1	Add Slice BAM by regions tool.	2012-05-02 11:32:19 -04:00
Jeremy Goecks	7c40df458e	Skeleton wrapper for Bowtie2.	2012-04-26 15:28:17 -04:00
Jeremy Goecks	64d1faeeb2	Add explicit Tophat2 wrapper.	2012-04-25 11:25:17 -04:00
Nate Coraor	cc2385220f	Miller Lab's Genome Diversity tools moved to the Tool Shed.	2012-04-09 13:13:44 -04:00
Daniel Blankenberg	195e08f2b1	Add GenomeSpace tools.	2012-03-29 10:24:28 -04:00
Daniel Blankenberg	d72a179e6e	Add FreeBayes to tool_conf.xml.main.	2012-03-27 18:09:55 -04:00
Richard Burhans	ff1b05d283	Updates to Human Genome Variation tools ... Rename Human Genome Variation to Phenotype Association	2012-03-22 13:03:01 -04:00
Greg Von Kuster	be1acc4d62	Eliminate the commented out emboss 5 tools from tool_conf.xml.sample.	2012-03-21 16:50:37 -04:00
Jeremy Goecks	693bc85d60	Add cuffmerge tool wrapper and functional test.	2012-02-01 22:36:17 -05:00
Daniel Blankenberg	043c0f39cf	Add a new complete FreeBayes tool configuration.	2012-02-01 11:25:18 -05:00
Daniel Blankenberg	718782e103	Add GATK Print Reads walker tool.	2012-01-24 16:29:28 -05:00
Daniel Blankenberg	ac5744c4d4	Add GATK VariantSelect tool.	2012-01-19 16:16:31 -05:00
Daniel Blankenberg	d59b7ec591	Add Maximal Information-based Nonparametric Exploration (MINE) tool.	2011-12-16 12:54:21 -05:00
Daniel Blankenberg	2351c4aaca	Add EBI ENA SRA tool contributed by Iain Cleland.	2011-12-13 09:45:49 -05:00
Daniel Blankenberg	46a7c49137	Temporarily remove Yogeshwar's recently added microsatellite tools from tool_conf.xml.sample to prevent buildbot testing.	2011-12-01 10:57:51 -05:00
Daniel Blankenberg	ace11b1edc	Fix tab to 4 spaces in tool_conf.xml.sample.	2011-11-29 17:07:06 -05:00
Richard Burhans	86fe959b0d	Added "Convert CG MasterVar file to pgSnp format" tool to the Human Genome Variation section	2011-11-28 13:13:39 -05:00
Daniel Blankenberg	7cf9b6daea	Updates for GenomeSpace file browser importer.	2011-11-21 17:12:07 -05:00
Daniel Blankenberg	8986dc2c81	Add SAMTools mpileup.	2011-11-21 16:30:34 -05:00
Daniel Blankenberg	d4f1f1e497	Update tool_conf.xml.sample.	2011-11-17 14:18:55 -05:00
Greg Von Kuster	4553be6460	Eliminate the non-functional PacBio tools from the distribution and the sample tool config.	2011-11-10 12:09:45 -05:00
Guruprasad Anada	08185087a7	Added 3 tools: 1) to compute weighted average values based on interval intersections (under Regional variation), 2) to perform logistic regression (under Multiple regression), 3) to compute partial R-squared (under Multiple regression).	2011-11-03 10:49:45 -04:00