Nicola Soranzo
3f103e2b38
Remove unused imports and unused variables. Fix spacing.
2014-01-27 19:51:46 +01:00
Dave Bouvier
b0efe4ddea
Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools.
2013-09-26 10:05:00 -04:00
James Taylor
d02155ad7b
Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5
2013-04-09 11:57:38 -04:00
Daniel Blankenberg
a422a9ed9f
Update Yogeshwar Kelkar's Microsatellite tools.
2013-01-11 09:48:47 -05:00
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
Guruprasad Anada
1d6a796f94
Suppressed R package-loading messages which were previously being written into stderr
2012-05-25 10:54:03 -04:00
Daniel Blankenberg
c1b4254ebe
Update Yogeshwar Kelkar's microsatellite tools.
2011-11-28 13:37:10 -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
Guruprasad Anada
5c978b62bd
Rounded the outputs of regression to 10 significant digits.
2011-06-27 15:44:59 -04:00
Nate Coraor
a221548e8f
An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.
2011-03-08 11:17:57 -05:00
Guruprasad Anada
4a81da484c
Updated tool help for microsatellite birth/death tools.
2011-03-07 13:30:37 -05:00
Nate Coraor
e3f970a36f
Use lines_diff on the pdf outputs of various R-based tools.
2011-03-03 12:21:44 -05:00
Guruprasad Anada
4a94876feb
Fixed functional test for 'compute q values' tool - q-value is rounded to 6 significant digits, which shouldn't differ between different runs of the tool.
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Also, fixed a bug in microsatellite birth/death tool - cases where microsatellite boundaries aren't defined are skipped.
2011-02-28 14:04:53 -05:00
Daniel Blankenberg
4eb1b0a79f
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
2011-02-28 12:16:28 -05:00
Guruprasad Anada
02ee54b502
Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool
2011-02-11 09:27:10 -05:00
Guruprasad Anada
924ea2443b
Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.
2011-02-10 10:33:08 -05:00
Dannon Baker
349d3a07bb
First pass standardizing to 'dataaset' from 'query'.
2011-01-27 13:46:20 -05:00
Guruprasad Anada
4d883c32db
Reverted 'fetch indels from 3-way alignments' tool to an earlier version (before rev 3707). Rev 3707 included changes made by Zaky from Makova lab, which caused some discrepancies in the output and have therefore been reverted back.
2011-01-25 14:17:20 -05:00
Guruprasad Anada
afc4bc7b60
Fixed a bug in microsatellite birth/death tool
2011-01-17 20:55:58 -05:00
Guruprasad Anada
8b7da7ec0e
Adding a new microsatellite birth/death analyser made by Yogeshwar from Makova lab.
2011-01-17 13:59:51 -05:00
Guruprasad Anada
1f12e6a3a5
Fixed bug in tool-dependency for "Extract orthologous microsatellites for multiple species alignments" tool.
2011-01-09 12:21:26 -05:00
Guruprasad Anada
c0192842b7
Adding a new microsatellite tool made by Yogeshwar from Makova lab.
2011-01-07 16:19:29 -05:00
Kanwei Li
2d0b8eb830
Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141
2010-12-14 14:22:13 -05:00
Nate Coraor
4d636f0562
Actually change the invocation of sputnik from bx-sputnik as mentioned in my last commit. Thanks Kanwei.
2010-10-07 16:50:37 -04:00
Nate Coraor
e05f11bc73
Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.
2010-10-07 16:23:57 -04:00
Nate Coraor
c09df6b5b2
Commit new versions of test outputs for some tools that use R and generate PDFs. The outputs are effectively the same but the actual PDF code varies slightly thanks to a newer version of R. Also, suppress noise in the compute_q_values tool that was causing its test to fail.
2010-09-28 17:05:36 -04:00
Dannon Baker
557396488e
Fix typo in Compute Motifs Frequency tool blurb.
2010-09-03 13:39:21 -04:00
Kanwei Li
4f291405f6
trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
...
- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track
- Minor grid refactoring
2010-08-26 12:12:32 -04:00
Kanwei Li
2b7726fb02
Don't pipe errors for compute_q_values to a file so we can find out what the error is
2010-08-19 17:03:54 -04:00
Guruprasad Anada
e62c1f3144
Adding new regional variation tools developed by Zaky from Makova lab.
2010-04-27 15:36:55 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Guruprasad Anada
45cffbb8ed
Added a new tool set for performing multivariate statistical analyses
2010-03-04 11:48:10 -05:00
Guruprasad Anada
22b3dfa1c2
Added functional tests for a couple of my tools with multiple outputs/pdf outputs.
2010-02-03 13:53:16 -05:00
Daniel Blankenberg
77bd226f2b
When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory.
2009-11-30 14:55:30 -05:00
Guruprasad Anada
049068730a
Added 'N' to the list of mask characters, as per Melissa's request.
2009-11-30 11:56:58 -05:00
Daniel Blankenberg
5927efceff
Remove metadata_source from quality_filter tool output. This will allow this tool to work on the cluster with external metadata and a readonly database/files filesystem. A better overall fix for setting external metadata files is in the works.
2009-11-20 16:22:04 -05:00
Kanwei Li
a947686b77
fix some typos for tools in folders N-Z
2009-09-25 02:06:03 -04:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Guruprasad Anada
f546868cf5
A tiny bug fix for linear regression tool.
2009-04-30 11:07:34 -04:00
Guruprasad Anada
55587fdb87
Added an option to mask non-CpG sites to the \"Mask CpG sites\" tool.
2009-04-27 11:59:42 -04:00
Guruprasad Anada
54667b80e6
Bug fixed in linear regression tool, and new option added to grouping tool.
2009-04-21 10:53:34 -04:00
Guruprasad Anada
280bd8e338
Modified help for \"get Indels\" tool, and made some small changes to the perl script.
2009-03-08 14:25:19 -04:00
Guruprasad Anada
b45b74f3ec
Fixes to get functional tests working.
2009-02-03 18:34:27 -05:00
Guruprasad Anada
41d1ce79c8
Removed lzo requirement from two tools- getIndels and qualityFilter.
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Also added validator to the regression tools.
2009-02-03 15:06:21 -05:00
Guruprasad Anada
1f62ffbb01
Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.
2009-01-27 16:17:22 -05:00
Guruprasad Anada
ee8779987e
More changes to mutability tool.
2009-01-15 13:10:04 -05:00
Guruprasad Anada
d46171ea21
Fixed a bug in microsatellite mutability tool.
2009-01-15 10:42:22 -05:00
Guruprasad Anada
e78f34fb49
Modified help message for indel rate tool.
2008-10-06 09:33:52 -04:00
Guruprasad Anada
0f1130e84a
Adding tools to fetch microsatellites and estimate their mutabilities.
2008-09-24 18:20:39 -04:00
Guruprasad Anada
9d3fd1eede
Modified INDEL tools under Regional variation section.
2008-09-22 12:02:35 -04:00
Nicola Soranzo