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

Removed lzo requirement from two tools- getIndels and qualityFilter.

2009-02-03 15:06:21 -05:00

categorize_elements_satisfying_criteria.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

categorize_elements_satisfying_criteria.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_motif_frequencies_for_all_motifs.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_motif_frequencies_for_all_motifs.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_motifs_frequency.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_motifs_frequency.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_q_values.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

compute_q_values.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

delete_overlapping_indels.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

delete_overlapping_indels.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

draw_stacked_barplots.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

draw_stacked_barplots.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -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

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00

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_3way.xml

Modified help for \"get Indels\" tool, and made some small changes to the perl script.

2009-03-08 14:25:19 -04:00

getIndels.py

Sync hashbangs

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

linear_regression.py

A tiny bug fix for linear regression tool.

2009-04-30 11:07:34 -04:00

linear_regression.xml

Added a new tool set for performing multivariate statistical analyses

2010-03-04 11:48:10 -05:00

maf_cpg_filter.py

Sync hashbangs

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

maf_cpg_filter.xml

Added 'N' to the list of mask characters, as per Melissa's request.

2009-11-30 11:56:58 -05:00

microsats_alignment_level.py

Adding tools to fetch microsatellites and estimate their mutabilities.

2008-09-24 18:20:39 -04:00

microsats_alignment_level.xml

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -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

parseMAF_smallIndels.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

quality_filter.py

Sync hashbangs

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

quality_filter.xml

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

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

Removed lzo requirement from two tools- getIndels and qualityFilter.

2009-02-03 15:06:21 -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

t_test_two_samples.pl

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

t_test_two_samples.xml

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

windowSplitter.py

Sync hashbangs

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

windowSplitter.xml

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00