galaxy

annotation_profiler

Add information for UCSC data to annotation profiler.

2011-11-16 10:40:55 -05:00

data_destination

merging from central

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

data_source

Updates for GenomeSpace file browser importer.

2011-11-21 17:12:07 -05:00

discreteWavelet

Update for wavelet variance tool contributed by Erika Kvikstad.

2011-08-30 09:33:10 -04:00

emboss_5

Add EMBOSS citation to EMBOSS tools.

2011-11-16 09:50:34 -05:00

encode

Tool help updates.

2011-09-21 04:11:07 -04:00

evolution

changed output type for aaChanges (from tabular to interval)

2011-09-26 15:59:52 -04:00

extract

(1) GFF parsing improvements; and (2) output improvements for extract genomic dna tool.

2011-08-14 19:49:26 -04:00

fasta_tools

Use fasta HDAs to specify custom builds. Do automatic conversions from fasta to 2bit and len; also, do conversion from len to linecount so that chrom/contig count is available. Finally, refactor 'compute fasta length' code out of tools and into converters.

2011-09-20 11:19:44 -04:00

fastq

Update FASTQ Groomer tool help to indicate that Illumina 1.8+ is Sanger encoded.

2011-11-08 16:53:19 -05:00

fastx_toolkit

Minor tool help updates.

2011-09-08 10:34:56 -04:00

filters

Tool help updates.

2011-11-14 13:26:29 -05:00

gatk

Remove no longer supported ROD datatypes from GATK tools (version 1.3).

2011-11-21 16:41:19 -05:00

genetrack

Update GeneTrack help.

2011-11-10 11:54:50 -05:00

genome_diversity

updated error handling for genome diversity select snps tool

2011-06-17 12:16:53 -04:00

human_genome_variation

Bug fixes for the ctd tool

2011-11-18 16:15:11 -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

MAF stats tool will now skip intervals with length less 1.

2011-09-23 09:36:57 -04:00

meme

Tool help updates.

2011-09-21 04:11:07 -04:00

metag_tools

Improve BLAST parser tool error handling, and improve elementtree import as well.

2011-07-12 18:14:56 -04:00

multivariate_stats

Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.

2011-07-15 10:33:02 -04:00

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

Improve BLAST parser tool error handling, and improve elementtree import as well.

2011-07-12 18:14:56 -04:00

new_operations

Trackster: enable tools that produce BED output to be used in visual analytics framework. Enable cluster tool in Trackster.

2011-09-19 11:59:09 -04:00

next_gen_conversion

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -05:00

ngs_rna

Update Cuffdiff test data to be compatible with v1.1.0

2011-11-18 15:14:39 -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

Tool help updates.

2011-11-14 13:26:29 -05:00

picard

Add picard_FastqToSam.xml and picard_SamToFastq.xml to tool_conf.xml.main.

2011-11-21 08:52:13 -05:00

plotting

Minor tool help updates.

2011-09-08 10:34:56 -04:00

regVariation

Added 3 tools: 1) to compute weighted average values based on interval intersections (under Regional variation), 2) to perform logistic regression (under Multiple regression), 3) to compute partial R-squared (under Multiple regression).

2011-11-03 10:49:45 -04:00

rgenetics

Fixes for the new horrible FastQC html layout. Now wastes a whole lot of space on the left

2011-11-16 07:34:51 +11:00

samtools

Update help for some SAMTools.

2011-11-21 16:55:16 -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

Velvet wrapper: fix typos, tabs -> spaces, spacing

2011-05-27 11:01:46 +02:00

sr_mapping

Update SRMA wrapper to use data tables.

2011-10-31 09:49:51 -04:00

stats

Grouping tool: make error clearer when a line doesn't have entry on grouped column

2011-10-04 23:11:23 -04:00

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

Fix for vcf_extract tool test

2011-03-02 09:40:10 -05:00

visualization

Minor tool help updates.

2011-09-08 10:34:56 -04:00