Dave Bouvier
35bc12d769
Migrate tools from the distribution to the tool shed.
2014-07-28 11:58:52 -04:00
John Chilton
f8bf5f4d8e
Merged in clayton_turner/galaxy-central (pull request #322 )
...
Added "ignore lines starting with specific characters" to group tool
2014-02-20 10:35:58 -06:00
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
Clayton Turner
fd85979a86
Fixed XML versioning and inputfile name
2014-02-14 12:25:20 -05:00
Clayton Turner
9e86f172bc
Merge from stable
2014-02-10 16:49:43 -05:00
Clayton Turner
7347d75a4a
Added ignore lines starting with specific characters to group tool
2014-02-10 16:00:30 -05:00
Daniel Blankenberg
3dbcdacfab
Fix for aggregate_scores_in_intervals.py broken in 95bf71620d50c6d81248eef2001a7dc156ae1088.
2014-01-27 09:54:34 -05:00
John Chilton
4fb2b89347
White-list expressions executed by filtering and dna_filtering tools.
2013-11-04 14:55:00 -05:00
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
John Chilton
53cb37aed3
Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
...
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html ).
There are still two copies.
2013-11-07 12:56:48 -05:00
John Chilton
73206460d6
Backed out changeset 9532e80796ec
2013-11-07 13:02:22 -05:00
John Chilton
4a3820ef58
Syncrhonize wiggle_to_simple.xml tool test cases, fix newlines.
...
As pointed by Peter (http://dev.list.galaxyproject.org/Bug-Two-copies-of-wiggle-to-simple-xml-tt4662486.html ).
There are still two copies.
2013-11-07 12:56:48 -05:00
John Chilton
be172fdfda
Merge Pull Request #244 .
2013-11-04 23:42:06 -06:00
Bjoern Gruening
b172b602ad
add [ and ] to mapped strings and advanced filters
2013-10-25 10:34:28 +02:00
Jeremy Goecks
502236ca2b
Import clean up and documentation for compute tool.
2013-03-18 10:09:43 -04:00
Jeremy Goecks
ea8d337316
Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.
2013-01-29 10:37:16 -05:00
Nate Coraor
8264b367fc
Add logical operators to the compute tool whitelist.
2012-10-08 10:28:29 -04:00
Nate Coraor
4fd61498ef
Fix the Compute tool to only allow for execution of a limited set of expressions.
2012-10-05 15:49:26 -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
Daniel Blankenberg
d59b7ec591
Add Maximal Information-based Nonparametric Exploration (MINE) tool.
2011-12-16 12:54:21 -05:00
Kanwei Li
8ef579f714
Grouping tool: make error clearer when a line doesn't have entry on grouped column
2011-10-04 23:11:23 -04:00
Nate Coraor
3cbde2e760
Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.
2011-08-24 14:38:29 -04:00
Kanwei Li
068ef1df40
Grouping tool: use system numpy if provided, otherwise use bundled numpy egg
2011-08-24 13:58:48 -04:00
Jeremy Goecks
a4b56c0b74
Improve filtering tool's stdout reporting of lines filtered; fixes #536
2011-06-15 13:22:18 -04:00
Kanwei Li
2f911c47ce
Improve docs for Grouping tool. Closes #576
2011-06-06 15:30:02 -04:00
Kanwei Li
a8ff1a91b3
Grouping tool:
...
- Converted to use numpy, which is included with Galaxy, instead of rpy, which is not.
- Don't simply skip lines if a numeric parameter encounters non-numeric data, return descriptive error with line contents instead
- General refactoring
- Added new comprehensive test, disabled until test framework supports multiple repeat inputs
2011-06-03 16:08:26 -04:00
Kanwei Li
34155271b3
[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535
2011-05-27 10:47:17 +02:00
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
Kanwei Li
82dde6e37e
Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
2011-03-22 17:49:09 -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
Guruprasad Anada
7c798f719a
Fixed ValueError being thrown by randint() function in group tool.
2011-01-28 10:42:08 -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
de36aa38a7
Add Standard deviation operation to grouping tool.
2010-12-09 11:43:54 -05:00
Jeremy Goecks
ccf07c72aa
Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.
2010-11-04 16:30:34 -04:00
Nate Coraor
8071eb8e13
Make r_wrapper.sh bourne/dash compatible.
2010-09-27 21:53:25 -04:00
Nate Coraor
e6afe5f830
Use a literal tab character instead of the bash $'\t' syntax in the grouping tool. This makes it compatible with bourne sh and dash.
2010-09-27 21:02:37 -04:00
Guruprasad Anada
d40c580de6
Modified Group tool by adding Mode function to the list of aggregate operations.
2010-07-29 12:21:09 -04:00
Daniel Blankenberg
36f7bcb0c8
Modify tools contributed by Chungoo Park (cxp440@psu.edu) for Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots; add a new tool to 'Generate A Matrix for using PC and LDA'; remove redundant 'Principal Component Analysis' tool.
2010-07-16 14:52:52 -04:00
Daniel Blankenberg
b3abddaa84
Update tests for pca_for_lda1 tool.
2010-05-27 11:29:20 -04:00
Daniel Blankenberg
1d87c0c5d4
Add tools contributed by Chungoo Park (cxp440@psu.edu) for Principal Component Analysis, Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots.
2010-05-25 15:48:25 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Greg Von Kuster
74b8ece4fc
Fix the column_maker tool so that if round is set to 'yes', the computed result is actually rounded. Added 2 new functional test to cover behavior.
2010-03-29 14:33:23 -04:00
Guruprasad Anada
9a6fb9b0a2
Import some math functions in 'Compute expression' tool.
2010-03-05 12:55:51 -05:00
Nate Coraor
0bfa58679b
Fix locations of cached data for tests
2010-02-25 12:27:07 -05:00
Kelly Vincent
5aa2ab1cb5
Corrected some typos in DNA filtering tool
2010-02-10 14:59:46 -05:00
Anton Nekrutenko
451a53cf89
Edites to DNA ambig filter interface
2010-02-10 14:42:42 -05:00
Kelly Vincent
269c7b36a7
Changed some of the filtering logic for DNA code filter tool, and got tests working
2010-02-10 13:18:45 -05:00
Kelly Vincent
0f8af048c5
Initial version of DNA code filter tool
2010-02-08 23:52:56 -05:00
Greg Von Kuster
a14492c491
Added from __future__ import division to the Filter tool and increased the version, and fixed the URL in the new bx_browser tool config.
2010-01-14 11:26:08 -05:00
Dave Bouvier