galaxy

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

Add metabolicMine datasource tool.

2011-02-09 15:42:42 -05:00

discreteWavelet

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

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

emboss_5

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

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

encode

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

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

evolution

Fixes to aaChanges tool

2010-12-02 13:04:05 -05:00

extract

Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.

2011-02-16 21:46:23 -05:00

fasta_tools

Fix typo in fasta/fastq to tabular converters

2010-12-10 16:29:03 -05:00

fastq

Do not print summary information in FASTQ groomer when grooming an empty file.

2011-02-18 12:07:27 -05:00

fastx_toolkit

Update FASTX tool wrappers to handle fastqsanger by passing -Q 33 to command-line as needed.

2011-01-27 09:54:53 -05:00

filters

Set output dataset type for 'Extract GFF features' tool to be input dataset type.

2011-02-22 18:41:15 -05:00

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

human_genome_variation

Initial commit of Mosaik and Freebayes.

2011-02-23 14:01:58 -05:00

hyphy

Added functional test for hyphy NJ tree builder.

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

indels

Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.

2010-09-27 21:35:03 -04:00

maf

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

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

meme

Add MEME tool configuration file.

2011-02-01 11:17:44 -05:00

metag_tools

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

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

multivariate_stats

Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca.

2011-02-22 12:37:06 -05:00

mutation

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

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

ncbi_blast_plus

Fix BLAST+ test

2011-02-24 15:07:46 -05:00

new_operations

Fix typo in Intersect tool description.

2011-02-18 10:42:13 -05:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Set default value for Cuffdiff's minimum alignment count parameter to reflect v0.9.3

2011-02-17 14:25:56 -05:00

ngs_simulation

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

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

peak_calling

Change method of accessing additional fields by name for dynamically generated select lists which was added in 4784:7be369e7cc6f.

2011-01-05 14:57:05 -05:00

plotting

Fixed functional tests for the following tools: histogram, estimate indel rates, compute q-values, kernel pca.

2011-02-22 12:37:06 -05:00

regVariation

Updated path to sputnik binary in 'Extract orthologous microsatellites for multiple (>2) species alignments' tool

2011-02-11 09:27:10 -05:00

rgenetics

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

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

samtools

Change output format of samtools flagstat from 'text' to 'txt'.

2011-01-26 15:45:27 -05:00

solid_tools

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

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

sr_assembly

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

sr_mapping

Initial commit of Mosaik and Freebayes.

2011-02-23 14:01:58 -05:00

stats

Fixed ValueError being thrown by randint() function in group tool.

2011-01-28 10:42:08 -05:00

taxonomy

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

2010-12-14 14:22:13 -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

vcf_tools

Adding ftype attribute to vcf tool tests

2011-02-24 12:16:33 -05:00

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