Jeremy Goecks
72f6f87644
Require pileup format as input to pileup parser tool.
2012-08-23 15:58:11 -04:00
Jeremy Goecks
41682ee6c9
Output sorted BAM from Bowtie2.
2012-08-22 16:49:12 -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
Richard Burhans
29d541c7be
name change: _BX main_ browser -> _BX_ table browser
2012-08-22 15:31:23 -04:00
Jeremy Goecks
66d1892364
More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs.
2012-08-21 16:54:19 -04:00
Jeremy Goecks
9fabf5dfbe
Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.
2012-08-16 16:32:00 -04:00
Jeremy Goecks
5c3fe00060
Include fusions output in Tophat2 wrapper.
2012-08-14 12:17:01 -04:00
Ross Lazarus
11349f28b5
Added unicode and raw flags to the re.sub string - not tested with unicode name yet..
2012-08-11 09:42:48 +10:00
Ross Lazarus
5238e15eb7
Unicode/raw for re.sub string in rgFastQC.py
2012-08-11 09:36:29 +10:00
Ross Lazarus
f2fa4636b6
Branch merge
2012-08-11 09:22:57 +10:00
Ross Lazarus
8bdddafc71
Add - and . to re.sub exclusion list for user supplied filename at Scott's suggestion and use _ as a substitute for
...
all other characters so
'cd \/; rm -rf'
becomes
'cd_____rm_-rf'
FastQC wrapper should now be reasonably hard to pervert but user filenames will be at least vaguely recognizable...
2012-08-11 09:21:45 +10:00
Nate Coraor
31c7003d4d
Merged in jmchilton/umn-galaxy-central/add_requirement_tags_for_plink (pull request #35 )
2012-08-10 14:33:59 -04:00
Ross Lazarus
5bdef6884b
Added sanitisation of the only user controllable parameter and removed use of shell in subprocess.popen to
...
improve security and reduce breakage risk from ugly filenames pointed out by A Nonymous in
https://bitbucket.org/galaxy/galaxy-central/issue/793/rgenetics-rgfastqcpy-tool-does-not-escape
2012-08-10 20:53:00 +10:00
Carl Eberhard
217690a63a
fix to mako import and some up-stack error reporting in tools
2012-08-08 12:30:25 -04:00
Scott McManus
e069425ab9
Removed offending code from last checkin - sorry for the foul-up
2012-08-07 13:35:39 -04:00
Jeremy Goecks
9a5679c37c
Use mako template in tool help so that dynamic image paths can be used. Fixes #141
2012-08-07 09:40:51 -04:00
Scott McManus
92915592f9
Added minor changes, including model accessors, for cancelling PBS tasks
2012-08-05 23:45:11 -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
Jeremy Goecks
0c00e50a54
Move implementation of from_work_dir attribute from job finish to job command line so that outputs are available earlier. This provides compatibility of attribute when setting metadata externally. Update Tophat wrapper to act as exemplar for attribute use.
2012-07-20 13:18:54 -04:00
Remi Marenco
dd7f9dc3a7
eXpress tool wrapped in Galaxy. Added in "NGS: RNA Analysis".
2012-07-17 17:12:51 -04:00
Greg Von Kuster
5c8fe01456
Migrate the freebayes tool out of the Galaxy code distribution.
2012-07-10 16:23:34 -04:00
Jeremy Goecks
6f2c3d6761
Have Bowtie2 wrapper produce BAM rather than SAM output.
2012-06-11 15:52:36 -04:00
Jeremy Goecks
ee9c75e09f
Handle Tophat2 fusion-ignore-chromosome parameter correctly.
2012-06-11 08:49:31 -04:00
Jeremy Goecks
0c12da85ba
Add min, max insert size parameters to bowtie2 wrapper.
2012-06-08 14:03:41 -04:00
Jeremy Goecks
a08c0c03ce
Fix bug in setting Bowtie2 parameters.
2012-06-08 13:48:37 -04:00
Ross Lazarus
c14fcf5ea0
Add some more missing quotes to command line.
2012-06-08 08:28:35 +10:00
Ross Lazarus
9fbf7007c7
Updates to fastqc tool to wrap the user supplied job name in quotes and sanitize to letters/digits only
...
Some downstream problems from ( characters reported today but probably needs deeper sanitizing
2012-06-08 08:26:09 +10:00
Jeremy Goecks
63fec8c332
Add preset alignment options to Bowtie2 wrapper and fix default in Tophat2 wrapper.
2012-06-06 15:27:59 -04:00
Jeremy Goecks
d802171ccb
Update default and help for Tophat2 coverage search parameter.
2012-06-06 14:42:21 -04:00
Jeremy Goecks
f7cfc540bd
Clarify inputs for forward, reverse reads in Tophat2 wrapper.
2012-06-04 09:29:51 -04:00
Jeremy Goecks
51312405f4
Add Bowtie2 preset options to Tophat2 wrapper.
2012-05-31 11:08:24 -04:00
Jeremy Goecks
2b023cc95f
Tophat2 wrapper updates: (a) use bowtie2-build; (b) add option to report discordant pairs; (c) update tests.
2012-05-31 10:08:13 -04:00
Jeremy Goecks
27f7aa9fde
Clearer explanation and help for default vs. full parameter settings.
2012-05-30 19:47:40 -04:00
Guruprasad Anada
1d6a796f94
Suppressed R package-loading messages which were previously being written into stderr
2012-05-25 10:54:03 -04:00
Jeremy Goecks
df28aec040
Full and proper sorting for GTF datasets: sort by, in order, transcript_id, chrom, and start.
2012-05-24 13:26:48 -04:00
Jeremy Goecks
35373ec78f
Merged in jmchilton/umn-galaxy-central/add_weblogo_requirement (pull request #33 )
2012-05-23 22:39:40 -04:00
Jeremy Goecks
4318998692
Merged in jmchilton/umn-galaxy-central/add_clustalw2_requirement (pull request #34 )
2012-05-23 22:39:00 -04:00
Daniel Blankenberg
89e347625f
Rewrite HbVar datasource tool.
2012-05-04 15:35:51 -04:00
Daniel Blankenberg
14734e345a
Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths.
2012-05-04 14:31:22 -04:00
Daniel Blankenberg
26e75b3e60
Allow GenomeSpace importer tool to sniff filetype when GSMetadata object is not available.
2012-05-03 12:25:06 -04:00
Daniel Blankenberg
c44aee110d
Update WormBase datasource tool to use WormBase 2.
2012-05-02 17:04:33 -04:00
Daniel Blankenberg
24e9b5df93
Fix typo in BAM slice tool.
2012-05-02 11:47:04 -04:00
Daniel Blankenberg
e8fe4c4dc1
Add Slice BAM by regions tool.
2012-05-02 11:32:19 -04:00
Jeremy Goecks
0cb9ceee2a
Revert Tophat wrapper version #.
2012-04-30 11:46:43 -04:00
Jeremy Goecks
f64f71e7ff
Revert Tophat wrapper due to parameter incompatibility issues.
2012-04-30 11:41:04 -04:00
Jeremy Goecks
9c7e7d8635
Merge
2012-04-29 20:34:39 -04:00
Jeremy Goecks
633c3cb9d5
Update Cuffdiff min-alignment-count default.
2012-04-28 22:21:30 -04:00
Jeremy Goecks
80f70cd0de
More cleaning of Tophat wrapper.
2012-04-27 15:22:11 -04:00
Jeremy Goecks
7c40df458e
Skeleton wrapper for Bowtie2.
2012-04-26 15:28:17 -04:00
Jeremy Goecks
78ce10ae5f
Remove version code from tophat wrappers as this is now handled by <version> tag.
2012-04-26 14:25:01 -04:00
Jeremy Goecks