Jeremy Goecks 72f6f87644 Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

..

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

name change: _BX main_ browser -> _BX_ table browser

2012-08-22 15:31:23 -04:00

discreteWavelet

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

encode

Tool help updates.

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

evolution

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

extract

Clean up temp files.

2012-03-09 16:11:21 -05:00

fasta_tools

Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.

2012-03-08 11:09:14 -05:00

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

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

filters

Add feature/attribute name indexing framework to converters. Provide full text indexing for GFF attributes.

2012-08-16 16:32:00 -04:00

gatk

Add argument names to parameter help for GATK tools' options.

2012-04-10 16:22:45 -04:00

genetrack

Update GeneTrack help.

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

genomespace

Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths.

2012-05-04 14:31:22 -04:00

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

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

meme

Specify meme requirement for fimo tool.

2012-02-02 21:29:30 -06:00

metag_tools

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -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

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

new_operations

fix to mako import and some up-stack error reporting in tools

2012-08-08 12:30:25 -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

Include fusions output in Tophat2 wrapper.

2012-08-14 12:17:01 -04:00

ngs_simulation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

peak_calling

Tool help updates.

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

phenotype_association

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

picard

Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py

2012-04-05 02:16:12 +10:00

plotting

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

regVariation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

rgenetics

More JS file reorganization: (a) move IE and rgenetics into their own directories; (b) move additional external libraries to libs.

2012-08-21 16:54:19 -04:00

samtools

Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

solid_tools

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

sr_assembly

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

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

sr_mapping

Output sorted BAM from Bowtie2.

2012-08-22 16:49:12 -04:00

stats

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

taxonomy

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

validation

…

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