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12,919 Commits 63 Branches 246 Tags
15aeb3f49ca8e67cb6afd0f034c2b5b6352e507b
Commit Graph
134 Commits
Author SHA1 Message Date
Dave Bouvier 2f2e163df7 Remove migrated tools from main's tool conf. 2014-04-01 11:05:31 -04:00
Nate Coraor 8331e4358d Remove empty/renamed sections in tool_conf.xml.main 2014-02-20 10:52:31 -05:00
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 51bcee1a9a One more tool removed in migration 9 that needed to be removed from tool_conf.xml.main. 2014-01-27 14:06:23 -05:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00
Nate Coraor a10abd381c Remove 4 tools from tool_conf.xml.main that were removed in migration 9. 2014-01-27 13:37:33 -05:00
Dave Bouvier a3914ad702 Remove migrated tools from tool_conf.xml.main 2014-01-27 09:53:51 -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
Daniel Blankenberg 186da8657e Add Pythonic FASTQ to FASTA converter back into tool_conf.xml.main removed in 10720:870b10eaa4cf. 2013-10-10 10:00:13 -04:00
Dave Bouvier 2e20f84d26 Remove migrated tools from tool_conf.xml.main. 2013-10-01 13:55:16 -04:00
Dave Bouvier 1f331f29e1 Remove migrated tools from tool_conf.xml.main. 2013-09-26 10:05:51 -04:00
Nate Coraor b741f55330 Remove unmaintained RGENETICS tools from Galaxy Main 2013-09-23 19:38:30 -04:00
Jeremy Goecks 8e35f124a4 Add Bowtie2 wrapper to main's tool conf. 2013-08-06 16:34:20 -04:00
Jeremy Goecks 20196a6e19 Add tophat2 to main tool conf. 2013-08-06 11:01:31 -04:00
Daniel Blankenberg a2a1a15b6f Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org). 2013-02-06 17:34:36 -05:00
Dave Bouvier 15443f2fa7 Updated tool_conf.xml.main with reverted migration. 2012-12-07 16:39:17 -05:00
Dave Bouvier 0ace24a2e0 Remove migrated tools from Galaxy main tool configuration. 2012-12-07 16:08:58 -05:00
Dave Bouvier 7b939369e1 Removed lastz and bowtie from tool_conf.xml.main 2012-11-26 10:20:38 -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
Daniel Blankenberg 0168740587 Add genomespace tools to tool_conf.xml.main. 2012-10-16 15:04:40 -04:00
Nate Coraor 2f3164649e Remove BWA from Main tool_conf. 2012-10-03 13:05:35 -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 af7cf227de Add BAM slicing tool to tool_conf.xml.main. 2012-06-07 10:06:43 -04:00
Nate Coraor 44d674e039 Moved Genome Diversity tools to toolshed, removed from main tool_conf. 2012-04-16 13:31:02 -04:00
Daniel Blankenberg d72a179e6e Add FreeBayes to tool_conf.xml.main. 2012-03-27 18:09:55 -04:00
Daniel Blankenberg aefabec0f0 Add FreeBayes to tool_conf.xml.main 2012-03-27 17:54:12 -04:00
Nate Coraor df0c22223a Remove the EMBOSS tools from Main's tool_conf. 2012-03-22 22:16:22 -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
Daniel Blankenberg 270ff535b1 Add GATK tools to tool_conf.xml.main. 2012-03-16 11:30:21 -04:00
Jeremy Goecks 693bc85d60 Add cuffmerge tool wrapper and functional test. 2012-02-01 22:36:17 -05:00
Daniel Blankenberg e342a19ad6 Add Perform Logistic Regression with vif, Compute partial R square, and Assign weighted-average to tool_conf.xml.main. 2012-01-25 12:56:09 -05:00
Daniel Blankenberg a29eb66d87 Add mpileup to tool_conf.xml.main. 2012-01-20 10:06:24 -05:00
Daniel Blankenberg 2351c4aaca Add EBI ENA SRA tool contributed by Iain Cleland. 2011-12-13 09:45:49 -05:00
Daniel Blankenberg 54b4dd64b5 Add picard_FastqToSam.xml and picard_SamToFastq.xml to tool_conf.xml.main. 2011-11-21 08:52:13 -05:00
Daniel Blankenberg 9b98a68127 Add Secure Hash/Message Digest tool to tool_conf.xml.main. 2011-10-11 10:09:32 -04:00
Daniel Blankenberg d3ef713d9b Add samtools rmdup tool. 2011-08-31 16:50:58 -04:00
Daniel Blankenberg 7607c57f24 Add SICER to tool_conf.xml.main. 2011-08-30 10:02:17 -04:00
Trevor Wennblom 424aca090e minor whitespace updates, tab/space consistency 2011-07-22 15:17:26 -05:00
Nate Coraor f62d8b581b Add Genome Diversity tools to Main 2011-06-16 09:54:30 -04:00
Nate Coraor b8fd7dbe2e Add Picard and fastqc tools to Main 2011-05-19 10:07:53 -04:00
Daniel Blankenberg 4bb2ac729b Update help and description for Draw ROC plot tool. Questions and comments should be directed to Chungoo Park. 2011-04-15 13:55:45 -04:00
Jeremy Goecks 1a371da9ae Add tool 'Filter GTF by attribute values list.' Tool filters a GTF based on a list of attribute values; this tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. Functional tests are included as well. 2011-04-11 09:39:55 -04:00
Kelly Vincent 8d6ec35964 Added BWA for SOLiD to tool_conf.xml.main 2011-04-06 16:28:33 -04:00
Ross Lazarus d6945af461 reverted unintended changes to tool_conf.xml.main 2011-04-05 14:14:08 -04:00
Ross Lazarus 70c8eccee0 change to weblogo test jpg comparison and code cleanups to rgCaCo 2011-04-05 14:07:10 -04:00
Nate Coraor 4d4f1763d8 Added clustalw and weblogo tools to Main tool_conf. Thanks Ross. 2011-04-05 12:08:42 -04:00