Daniel Blankenberg 64c68b5a66 Several Fixes for Uploading Composite datatypes. Revert changeset 3769:69e70e588a8e.

2010-05-12 15:57:05 -04:00

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annotation_profiler

Updates for 'Profile Annotations for a set of genomic intervals' tool. This tool will now report a 'data version'. Add a script that creates the indexes and table description xml from a UCSC database dump.

2010-04-23 11:14:26 -04:00

data_destination

merging from central

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

data_source

Several Fixes for Uploading Composite datatypes. Revert changeset 3769:69e70e588a8e.

2010-05-12 15:57:05 -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 additional tests to FASTQ Quality Trimmer tool

2010-04-09 11:35:02 -04:00

fastx_toolkit

Fix accidentally committed fastx tool configs

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

filters

GTF to BEDGraph converter.

2010-04-22 16:05:08 -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

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

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

Enhanced column join to allow user to specify fill values for empty columns, either one value for all or by column

2010-05-05 11:34:29 -04:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Add 'filter transcripts via tracking' tool to RNA-seq tools. This tool is useful for operating on output files from cufftools suite.

2010-05-10 12:42:05 -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

Add mimetypes to snp/wga datatypes in genetics.py

2010-05-11 11:51:49 -04:00

samtools

Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.

2010-04-30 15:27:41 -04:00

solid_tools

Sync hashbangs

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

sr_mapping

Fix dbkey setting for BWA.

2010-04-30 15:45:32 -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

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