galaxy

best_regression_subsets.py

Adding a new set of toolss to perform multiple linear regression analysis.

2008-09-20 18:14:24 -04:00

best_regression_subsets.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

compute_q_values.pl

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.

2011-02-28 14:04:53 -05:00

compute_q_values.xml

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

featureCounter.py

Bug fixes, miscellaneous cleanup for flanking_features, windowSplitter, quality_filter, featureCounter, get_flanks.

2008-05-27 14:28:49 +00:00

featureCounter.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

getIndelRates_3way.py

Modified INDEL tools under Regional variation section.

2008-09-22 12:02:35 -04:00

getIndelRates_3way.xml

Modified help message for indel rate tool.

2008-10-06 09:33:52 -04:00

getIndels_2way.xml

Added tool dependencies to xml.

2008-04-25 19:40:16 +00:00

getIndels.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

linear_regression.py

Rounded the outputs of regression to 10 significant digits.

2011-06-27 15:44:59 -04:00

linear_regression.xml

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

logistic_regression_vif.py

Suppressed R package-loading messages which were previously being written into stderr

2012-05-25 10:54:03 -04:00

logistic_regression_vif.xml

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

maf_cpg_filter.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

maf_cpg_filter.xml

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

microsats_alignment_level.py

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

microsats_alignment_level.xml

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

microsats_mutability.py

More changes to mutability tool.

2009-01-15 13:10:04 -05:00

microsats_mutability.xml

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

partialR_square.py

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

partialR_square.xml

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

quality_filter.py

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

quality_filter.xml

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

qv_to_bqv.py

Removed the remainder of the tool version subdirectories.

2008-03-03 18:38:57 +00:00

qv_to_bqv.xml

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

rcve.py

Adding a new set of toolss to perform multiple linear regression analysis.

2008-09-20 18:14:24 -04:00

rcve.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

substitution_rates.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

substitution_rates.xml

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

substitutions.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

substitutions.xml

Adding tools to compute Substitution rates.

2008-09-21 17:36:28 -04:00

WeightedAverage.py

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

WeightedAverage.xml

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

windowSplitter.py

Sync hashbangs

2010-04-01 20:36:31 -04:00

windowSplitter.xml

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00