galaxy

2010-02-25 12:27:07 -05:00

2008-10-28 11:28:15 -04:00

Fix bug in upload where source import files could be removed if an error occurs during detection and galaxy owns the source files.

2010-03-23 12:45:08 -04:00

emboss_5

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

encode

Fix gencode partition tool to not use hard-coded paths.

2009-12-09 15:21:41 -05:00

evolution

Changing an 'and' to 'or' in SNP mutate codon tool error checking.

2009-09-22 11:40:41 -04:00

extract

Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling.

2010-03-10 11:51:00 -05:00

fasta_tools

Fix fast_compute_length performance by using version contributed by Bjoern Gruning, and fix email configuration bug in the user controller which was found by Ed Kirton.

2010-01-25 10:01:04 -05:00

fastq

Update tool_conf.xml.main to use the new FASTQ tools. Minor updates to help text for a few of the FASTQ tools.

2010-03-03 15:18:09 -05:00

fastx_toolkit

Fix accidentally committed fastx tool configs

2010-01-07 16:20:04 -05:00

filters

Fix locations of cached data for tests

2010-02-25 12:27:07 -05:00

genetrack

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -05:00

maf

Update tool tests for MAF to interval tool

2010-03-09 14:29:17 -05:00

metag_tools

Fix locations of cached data for tests

2010-02-25 12:27:07 -05:00

multivariate_stats

Updated functional tests for \"multivariate statistics\" tools, by shortening the number of decimal places displayed, so that they pass on all test platforms.

2010-03-10 16:23:53 -05:00

new_operations

Enhance functional test framework so that a boolean form field ( checkbox ) can have a false value ( be unchecked ). Add a 2nd test to gops_concat that uses this behavior.

2010-02-17 11:07:08 -05:00

next_gen_conversion

Fixed my previous fix for copying history items to a library, which really didn't fix anything. ¬†Fixed the functional tests for lav_to_bed, split_paired_reads, and solid2fastq by adding the 2nd output dataset to the test for each tool. ¬†Renamed the test files for the tools to have the Galaxy supported file extension.

2010-01-14 09:44:58 -05:00

peak_calling

Update tests for MACS peakcaller.

2010-03-08 14:35:56 -05:00

plotting

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

regVariation

Added a new tool set for performing multivariate statistical analyses

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

samtools

Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling.

2010-03-10 11:51:00 -05:00

solid_tools

fix some typos for tools in folders N-Z

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

sr_mapping

First pass as PerM. Also made cosmetic changes to BWA.

2010-03-17 16:40:36 -04:00

stats

Import some math functions in 'Compute expression' tool.

2010-03-05 12:55:51 -05:00

taxonomy

Bug fixes to LCA tool

2010-02-22 16:22:12 -05:00

validation

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

visualization

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00