Jeremy Goecks bb984db3c2 Fix options bug in cufflinks wrapper.

2010-06-17 09:14:58 -04:00

..

annotation_profiler

Resync Annotation Profiler tests to current cached data.

2010-06-02 16:40:39 -04:00

data_destination

merging from central

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

data_source

Patch to upload.py for composite file uploads where the user supplies urls for components

2010-06-11 21:21:33 -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

Allow FASTQ Groomer/parser to work on tab-delimited decimal scores.

2010-05-24 15:33:55 -04:00

fastx_toolkit

Fix accidentally committed fastx tool configs

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

filters

Add colon as a delimiter for 'Convert delimiters to TAB' tool.

2010-06-09 10:27:01 -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

Add a VCF to MAF Custom Track converter tool. This tool converts a Variant Call Format (VCF) file into a Multiple Alignment Format (MAF) custom track file suitable for display at genome browsers.

2010-06-14 15:07:46 -04:00

metag_tools

Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output

2010-04-12 15:56:13 -04:00

multivariate_stats

Fixed functional tests for kcca, linear regression and get indels tools. Have used 're_match' to accommodate sign and decimal precision changes in kcca output.

2010-06-09 12:52:47 -04:00

new_operations

Fixed a bug in 'Fetch closest features' tool that prevented fetching of immediately adjacent features.

2010-06-16 15:50:38 -04:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Fix options bug in cufflinks wrapper.

2010-06-17 09:14:58 -04:00

peak_calling

Add eland and elandmulti formats. Enhance MACs peakcaller to properly handle these formats.

2010-04-27 10:59:46 -04:00

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

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

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

rgenetics

More functional test tweaks - pdf sizes are vastly different on solaris for rgManQQ and rgQC

2010-05-24 21:29:14 -04:00

samtools

Fixed handling of alignments with CIGAR strings with multiple indels for SAM indel filter, plus updated test files

2010-06-10 13:19:43 -04:00

solid_tools

Sync hashbangs

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

sr_assembly

Add support for velvet data types and velveth and velvetg tool wrappers, all contributed by James E Johnson - University of Minnesota.

2010-06-09 11:23:10 -04:00

sr_mapping

Fix dbkey setting for BWA.

2010-04-30 15:45:32 -04:00

stats

Update tests for pca_for_lda1 tool.

2010-05-27 11:29:20 -04:00

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