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
Daniel Blankenberg
5d964a4a24
Add Picard tools FASTQ to SAM (makes BAM) tool. Add Picard tools SAM to FASTQ tool.
2011-10-24 16:11:20 -04:00
Daniel Blankenberg
e8d8d8e7c3
Add test/development GenomeSpace file importer datasource tool.
2011-10-06 13:55:25 -04:00
Kanwei Li
fec37cd896
Standardize {datatypes|tool}_conf.xml.sample with 2 space indentation and newline before <label> blocks
2011-10-04 23:29:08 -04:00
Jeremy Goecks
b996bd89dd
Comment the Trinity assembler out of the sample tool conf so that it must be explicitly enabled.
2011-09-15 17:10:39 -04:00
Daniel Blankenberg
9017c6fbd8
Add tool for calculating Secure Hashes / Message Digests of a dataset using the user selected algorithms.
2011-09-09 12:01:43 -04:00
Daniel Blankenberg
d301e2cd57
Update existing GATK tools. Add 4 new GATK tools: VariantAnnotator, VariantFiltration, VariantRecalibrator, ApplyRecalibration, ValidateVariants, VariantEval and CombineVariants. All GATK tool wrappers are still considered BETA and (workflow/rerun/etc) backwards-incompatible changes should be expected.
2011-09-01 11:08:34 -04:00
Daniel Blankenberg
d3ef713d9b
Add samtools rmdup tool.
2011-08-31 16:50:58 -04:00
Daniel Blankenberg
246edd5590
Add wavelet variance tool contributed by Erika Kvikstad.
2011-08-29 11:22:54 -04:00
Daniel Blankenberg
19ed039b6c
Add SICER peak caller.
2011-08-26 15:53:16 -04:00
Daniel Blankenberg
ed79503fe7
Add FIMO to tool_conf.xml.sample.
2011-08-22 14:58:51 -04:00
Jeremy Goecks
781cef42bd
Add wrapper for Trinity, the de novo RNA-seq transcript assembler ( http://http://trinityrnaseq.sourceforge.net/ ).
2011-08-18 14:20:48 -04:00
Ross Lazarus
5b2e7947ea
Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.
...
Changes to rgManQQ so the user can obtain a decent pdf image. When millions of points are plotted, these are humongous so GS is called to compress the resulting pdf and they are now of reasonable size. PDF's are now linked from the thumbnails. Some minor fiddling with point size on the Manhatten plots so the intersting ones are a little more obvious.
Minor tweak to twilltestcase.py so composite file components are copied correctly to the directory specified by GALAXY_TEST_SAVE. This makes updating test artefacts much simpler because running tests with GALAXY_TEST_SAVE pointing somewhere will now save every tested output file.
2011-08-04 12:43:30 +10:00
Ross Lazarus
0f1c751800
fixes for rgManQQ plots to create a compressed PDF using GS as the downloadable artifact - much more useful for publication
2011-08-04 10:57:03 +10:00
Trevor Wennblom
424aca090e
minor whitespace updates, tab/space consistency
2011-07-22 15:17:26 -05:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
...
This is a backout of commit 5765
2011-07-06 09:44:56 +10:00
Ross Lazarus
86b55bb0c0
branch merge
2011-07-05 12:40:43 +10:00
Kelly Vincent
20f77b2a71
Added color-space Tophat wrapper
2011-06-24 16:55:43 -04:00
Richard Burhans
b94760d1eb
uncommented genome diversity tools
2011-06-15 17:16:23 -04:00
Greg Von Kuster
3871eef144
Add Pacific Biosciences tools.
2011-06-14 16:42:11 -04:00
Florent Angly
cdde306069
FASTQ interlacer and de-interlacer tools fully integrated in Galaxy and functional
2010-12-17 15:04:17 +10:00
Ross Lazarus
e0545fcd8f
separated ngs picard tools and removed fastqc wrapper lgpl annotation
2011-05-17 12:52:24 -04:00
Daniel Blankenberg
364180ef7d
First pass at adding some GATK tools. Included tools are "Realigner Target Creator", "Indel Realigner", "Count Covariates", "Table Recalibration", "Analyze Covariates" and "Unified Genotyper". These tool integrations should be considered beta: changes that will not be backwards-compatible with workflows and re-run functionality should be expected.
...
TODO:
A few new datatypes have been declared, but exist in name only (subclasses of Text defined only in datatypes_conf.xml), these should be refined to be true datatypes, with proper peeks, sniffing, metadata, etc.
Help sections need work.
HTML listing of files in e.g. Analyze Covariates should be prettified.
Other items not listed.
2011-05-11 09:38:23 -04:00
Ross Lazarus
b4c000956e
lots of small tweaks and some new picard metrics - Hs and libcomplexity. Includes an option to use the input data genome for a reference where a reference genome is needed - helps prevent new user head scratching - this really should be added (eg) the bwa and other wrappers too?
2011-05-07 11:56:12 -04:00
Nate Coraor
50ea0e1471
Fix a typo in the sample tool_conf.xml, thanks Marina Gourtovaia.
2011-05-06 12:09:58 -04:00
Guruprasad Anada
0409faf4ee
Commented out 'Wavelet analysis' section from tool_conf.xml.sample - will be reverted once functional tests are written for these tools.
2011-05-06 10:28:54 -04:00
Ross Lazarus
9e9ecece8b
an errant == in tool_conf.xml.sample fixed
2011-04-28 09:33:19 -04:00
Ross Lazarus
32f2177838
missing slash in tool_conf.xml.sample fixed
2011-04-28 09:17:50 -04:00
Ross Lazarus
a33ddf3154
uncommented new tools in tool_conf.xml.sample so buildbot can find them and explanation when insertsizemetrics fails
2011-04-27 17:06:14 -04:00
Ross Lazarus
bd2a16bc47
Large push with modifications to the Picard tools recently added plus 5 new ones
...
and tests
Also includes fastqc which is a very comprehensive QC report generator for
sam/bam and fastq
2011-04-27 12:41:57 -04:00
Kelly Vincent
ade61dc51a
Initial commit with 5 Picard tools (AddOrReplaceReadGroups, BamIndexStats, MarkDuplicates, ReorderSam, ReplaceSamHeader). Test files are included but currently those with bam output are commented because they are failing tests but working in the browser.
2011-04-22 15:10:04 -04:00
Richard Burhans
6945b821f4
added a commented-out section for the genome diversity tools
2011-04-21 17:29:41 -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
Ross Lazarus
6646cfa80d
Adding two new tool wrappers and tests - clustalw ( http://www.clustal.org ) for multiple alignments and a sequence motif generator based on weblogo3 ( http://weblogo.berkeley.edu ) which works on fasta files such as alignments from clustalw
2011-03-22 14:08:32 -04:00
Jeremy Goecks
f6a601f517
Add count GFF features tool and tests. Tool counts the number of features in a GFF file; this is different than the number of lines b/c GFF features are often multiline.
2011-03-21 13:01:24 -04:00
Daniel Blankenberg
a01df218d7
Update CCAT to version 3.0.
2011-03-16 10:41:38 -04:00
Ramkrishna Chakrabarty
58284e4848
Adding tests for vcf extract and filter tools
2011-02-28 15:03:45 -05:00
Jeremy Goecks