Jeremy Goecks afbf065eb3 Tophat2 wrapper update: (a) remove unneeded wrapper script; and (b) use stdio tags to capture and show output; and (c) update functional tests for most recent version of Tophat.

2013-05-06 14:40:44 -04:00

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annotation_profiler

Add information for UCSC data to annotation profiler.

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

data_destination

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data_source

Merged in nsoranzo/galaxy-central (pull request #135)

2013-04-04 08:41:54 -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

Make wrapper compatible with python 2.5.

2013-01-23 12:32:05 -05:00

extract

Replaced "query" with "dataset" in a number of tool definition XML files.

2013-01-14 16:13:54 -08:00

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

tool tip fix for fastq summary and sorter

2013-03-19 11:50:03 -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

grep/select tool: fixed tab-delimiter matching for GNU version of grep

2013-04-02 15:18:22 -04:00

gatk

Covert more duplicated GATK wrapper code to macros.

2013-03-22 00:41:08 -05:00

genetrack

Update GeneTrack help.

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

genomespace

Update GenomeSpace tools to use __user__ as needed.

2013-05-03 16:02:40 -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

Make maf-to-bed object-store aware

2013-03-06 12:40:31 -05:00

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

Subtract query tool: make ignoring empty end columns and whitespace optional.

2013-02-07 14:46:49 -05:00

next_gen_conversion

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

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

ngs_rna

Tophat2 wrapper update: (a) remove unneeded wrapper script; and (b) use stdio tags to capture and show output; and (c) update functional tests for most recent version of Tophat.

2013-05-06 14:40:44 -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

Update functional test parameters so tests will pass.

2013-01-22 15:54:49 -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

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

rgenetics

Remove unused test parameter.

2013-01-14 14:00:21 -05:00

samtools

Require pileup format as input to pileup parser tool.

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

solid_tools

Fix tool tip for compute quality statistics

2013-03-19 12:04:24 -04:00

sr_assembly

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

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

sr_mapping

Change order of Bowtie2 output datasets to put aligned reads at top of history.

2013-01-30 12:55:49 -05:00

stats

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -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

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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