Daniel Blankenberg dce29408d6 Add FASTQ Quality Trimmer by sliding window tool.

2010-04-08 15:25:38 -04:00

..

annotation_profiler

Fix locations of cached data for tests

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

data_destination

merging from central

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

data_source

Fixes to rgQC top table ordering and add offset so can use rgManQQ to make plots

2010-04-05 14:14:09 -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

Next rev of codingSnps tool.

2010-03-24 14:14:58 -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

Sync hashbangs

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

fastq

Add FASTQ Quality Trimmer by sliding window tool.

2010-04-08 15:25:38 -04:00

fastx_toolkit

Fix accidentally committed fastx tool configs

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

filters

sff converter tool

2010-04-07 11:12:00 -04:00

genetrack

Add bed6 and bed12 datatypes, which are subclasses of bedstrict; converters are available to turn any interval datatype into these types. Change GeneTrack Indexer tool and converter to use bed6 as input.

2010-04-01 13:08:48 -04:00

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

Sync hashbangs

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

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

Sync hashbangs

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

next_gen_conversion

Updated output format for solid2fastq converter

2010-04-07 08:44:57 -04:00

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

Sync hashbangs

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

rgenetics

Fixes to rgQC top table ordering and add offset so can use rgManQQ to make plots

2010-04-05 14:14:09 -04:00

samtools

Updated output format for solid2fastq converter

2010-04-07 08:44:57 -04:00

solid_tools

Sync hashbangs

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

sr_mapping

Sync hashbangs

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

stats

Sync hashbangs

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

taxonomy

Bug fixes to LCA tool

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

tophat

Sync hashbangs

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

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