galaxy

Add information for UCSC data to annotation profiler.

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

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

Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API

2012-10-04 15:31:16 -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

updates to Phenotype Association tools from Belinda

2012-11-20 11:42:13 -05:00

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

Fix for fastq filter tests of paired_end boolean.

2012-09-14 15:50:38 -04:00

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

Revert tool migration.

2012-12-07 16:38:26 -05:00

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

Enhance GenomeSpace filebrowser importer to display a better history item name for additional primary datasets.

2012-10-24 12:33:34 -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

Fixed error in solid2fasta.xml preventing help text from displaying.

2012-09-04 10:15:18 -04:00

ngs_rna

Update Cuff* labels to reflect GFF3 compatibility.

2012-12-04 09:09:36 -05:00

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

updates to Phenotype Association tools from Belinda

2012-11-20 11:42:13 -05:00

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

Fix parameters for fastqc to work properly with bam and with a contaminants file

2012-10-26 16:00:13 +11:00

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

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

stats

Add logical operators to the compute tool whitelist.

2012-10-08 10:28:29 -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

Performance enhancements for Build custom track for UCSC genome browser tool.

2012-10-16 15:25:01 -04:00