John Chilton
892912c02d
Merged in abrenner/galaxy-central (pull request #215 )
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histogram2 - RPY requires R - missing from requirements tag
Thanks for the contribution!
2013-10-16 22:12:40 -05:00
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
Adam Brenner
35d32232d4
histogram2.xml python module rpy requires R package.
2013-09-12 18:36:20 +00:00
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
Daniel Blankenberg
a6ecae74fd
Minor tool help updates.
2011-09-08 10:34:56 -04:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
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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
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
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
ff7e8fe2e0
Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca.
2011-02-22 12:37:06 -05:00
Nate Coraor
409f149aa4
Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson.
2011-02-03 15:52:44 -05:00
Dannon Baker
349d3a07bb
First pass standardizing to 'dataaset' from 'query'.
2011-01-27 13:46:20 -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
Daniel Blankenberg
8e42a241d6
Enhance histogram tool to allow plotting as frequency/counts.
2010-12-09 15:39:58 -05:00
Anton Nekrutenko
2763d08d86
Modified help section and help tags to ease paremeter selection by the user
2010-12-03 09:57:45 -05:00
Daniel Blankenberg
00306e15ed
Make boxplot tool respect exit codes when determining job errors: makes e.g. 'Could not find/open font when opening font "arial", using internal non-scalable font' a non-fatal warning. Add version attribute to gnuplot requirement tag.
2010-03-22 11:06:40 -04:00
Daniel Blankenberg
4cb98d8b5f
Add gnuplot requirement tag to boxplot tool.
2010-02-23 19:54:54 -05:00
Daniel Blankenberg
8082c6f36f
Add a new FASTQ tool suite. Four FASTQ variants are supported: sanger, illumina, solexa and solid.
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Tools include:
FASTQ Groomer convert between various FASTQ quality formats
Combine FASTA and QUAL into FASTQ
FASTQ joiner on paired end reads
FASTQ splitter on joined paired end reads
FASTQ to FASTA converter
FASTQ Summary Statistics by column
Filter FASTQ reads by quality score and length
FASTQ Trimmer by column
Manipulate FASTQ reads on various attributes
Boxplot of quality statistics (Generic, with outliers)
2010-02-23 16:48:07 -05:00
Nate Coraor
65d3ad47cd
Fix from Assaf Gordon for Cheetah syntax errors in the Bar Chart tool.
2010-02-08 10:00:30 -05:00
Guruprasad Anada
ae3e0763b9
Updating histogram functional test output, which had changed as a result of R version upgrade.
2009-12-14 15:17:13 -05:00
Greg Von Kuster
eca5a69f9f
Update the output test dataset for the XY_Plot_1 tool due to a new version of R, and update the tool version so the functional test will pass.
2009-12-10 09:18:49 -05:00
Daniel Blankenberg
f92b25d2f5
Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .
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Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.
Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.
Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
2009-12-07 10:19:41 -05:00
Guruprasad Anada
bcd0192709
Fix bar chart output format.
2009-08-03 16:38:27 -04:00
Guruprasad Anada
167ce59b29
Bug fixes for histogram liftover and grouping tools.
2009-05-29 11:07:18 -04:00
Guruprasad Anada
fa533faa95
push changesets to security from central
2009-03-05 13:09:02 -05:00
Guruprasad Anada
ebeece6204
Adding a tiny fix to scatter plot tool.
2009-03-05 13:02:17 -05:00
Anton Nekrutenko
43891dced2
updated bar charter to use png instead of pdf
2009-01-22 12:06:29 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Guruprasad Anada
9887101d60
Fix for scatterplot.py: Handling an uncaught exception.
2008-09-08 14:36:37 -04:00
Greg Von Kuster
04e0834500
Revert 2715.
2008-06-04 13:02:15 +00:00
Greg Von Kuster
dedc7278a1
Requires config change, temporary files are now created in a configurable location - affects many tools.
2008-06-03 20:29:54 +00:00
Nate Coraor
f53cb1d7f1
Added tool dependencies to xml.
2008-04-25 19:40:16 +00:00
Greg Von Kuster
1580ed8260
Functional tests will now properly handle output datasets in pdf format. Added functional tests for histogram and scatterplot. Fixed a bug where temporary files was not removed if functional test failed.
2008-04-04 14:45:29 +00:00
Greg Von Kuster
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +00:00
Greg Von Kuster
69a20f0fa7
Corrected old directions on several tools.
2008-03-13 20:46:43 +00:00
Anton Nekrutenko
2ca6d902fe
Changes to bar chart tool
2008-03-11 12:54:47 +00:00
Anton Nekrutenko
f92ff79502
Changes to bar chart tool
2008-03-11 12:45:55 +00:00
Anton Nekrutenko
85cebb59b6
Bar chart tool for use with taxonomy tools. Requires gnuplot and gnuplot.py. Still needs interface testing
2008-03-10 21:57:32 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
218684f610
Added tool version directories for plotting tools directory.
2008-02-22 19:41:52 +00:00
Greg Von Kuster
4fda68c476
Bug fix in histogram tool.
2007-12-11 21:41:31 +00:00
Greg Von Kuster
fb569d3c43
More ColumnListParameter cleanup. Eliminated dynamic options from some tools by using ColumnListParameter.
2007-10-18 17:29:47 +00:00
Greg Von Kuster
4f8eb6578b
Various tool fixes, eliminated now unnecessary "refresh_on_change", eliminated old aggregation tool, fixed db conditional in mapping.
2007-10-12 13:11:17 +00:00
James Taylor
13608b5a8b
Cleaning up ColumnListParameter and related things.
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- Dependencies between parameters and refresh_on_change are now more general.
Any parameter can assert a dependency on any other parameter by name, and
if a parameter has dependencies it will cause a refresh.
- Use "other_values" to get at the value of the associated dataset rather
than trying to look at the tool. This means that column lists now work
inside grouping constructs.
- Eliminated tool.updated_params and use of self.legal_values. These
variables are GLOBAL. Everybody using a tool has a reference to the same
instance of tool. Thus, if two people are using the same tool at once this
can cause serious problems.
2007-10-08 19:33:23 +00:00
Greg Von Kuster
23fd74c2c5
Better error handling for tools that use columnlist tool parameter.
2007-09-19 14:49:02 +00:00
Greg Von Kuster
50968827e9
Enhanced sort tool to use columnlist tool parameter, altered functional test to work with new version. Some other miscellaneous cleanup.
2007-09-17 20:48:59 +00:00
Greg Von Kuster
6ebc7a706e
Fixed scatterplot tool to use ColumnList parameter and deleted some unused files.
2007-09-07 13:58:08 +00:00
Greg Von Kuster
c3538a55b7
Enhanced histogram tool to use new columnlist parameter and cleaned up the tool code.
2007-09-04 20:16:33 +00:00
Greg Von Kuster
fcf736f990
Some bug fixes. The fixes to scatterplot and cor code will eventually be replaced with a new approach to building column select lists.
2007-08-22 20:06:47 +00:00
Greg Von Kuster
312620d2eb
Fixes to various tools: scatterplot, cor, grouping
2007-08-21 14:55:36 +00:00
John Chilton