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

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

Fix typo in Compute Motifs Frequency tool blurb.

2010-09-03 13:39:21 -04:00

compute_q_values.pl

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

compute_q_values.xml

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

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

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

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_3way.xml

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

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

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

2011-01-27 13:46:20 -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

microsatellite_birthdeath.pl

Fixed a bug in microsatellite birth/death tool

2011-01-17 20:55:58 -05:00

microsatellite_birthdeath.xml

Adding a new microsatellite birth/death analyser made by Yogeshwar from Makova lab.

2011-01-17 13:59:51 -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

multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl

Fixed bug in tool-dependency for "Extract orthologous microsatellites for multiple species alignments" tool.

2011-01-09 12:21:26 -05:00

multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml

Adding a new microsatellite birth/death analyser made by Yogeshwar from Makova lab.

2011-01-17 13:59:51 -05:00

parseMAF_smallIndels.pl

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

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

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

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

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

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