Daniel Blankenberg 2d5b8eca2f Add argument names to parameter help for GATK tools' options.

2012-04-10 16:22:45 -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

Add GenomeSpace tools.

2012-03-29 10:24:28 -04:00

discreteWavelet

Update for wavelet variance tool contributed by Erika Kvikstad.

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

encode

Tool help updates.

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

evolution

changes to aaChanges interface

2012-04-02 14:28:08 -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

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

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

Small fix for setting upload path in GenomeSpace export tool.

2012-03-30 17:08:35 -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

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

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

meme

Specify meme requirement for fimo tool.

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

metag_tools

Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.

2011-11-29 17:30:14 -05:00

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

BLAST wrappers: Split FASTA query into parts

2012-02-17 12:24:01 +00:00

new_operations

Have GOPs Concatenate tool always respect the provided strand column.

2012-01-18 10:30:08 -05:00

next_gen_conversion

Update links to reflect Galaxy Wiki moving away from Bitbucket.

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

ngs_rna

Add necessary space after threads option in Cuffmerge.

2012-03-08 08:37:20 -05:00

ngs_simulation

Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.

2011-11-29 17:30:14 -05:00

peak_calling

Tool help updates.

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

phenotype_association

Add FreeBayes to tool_conf.xml.main.

2012-03-27 18:09:55 -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

Minor tool help updates.

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

regVariation

Update Yogeshwar Kelkar's microsatellite tools.

2011-11-28 13:37:10 -05:00

rgenetics

Updates to FastQC wrapper

2012-02-10 10:40:00 +11:00

samtools

Fix inconsequential warning about when tag when loading samtools mpileup.

2012-04-10 16:07:19 -04:00

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

Fix for BWA -R option.

2012-04-10 09:24:25 -04:00

stats

Add Maximal Information-based Nonparametric Exploration (MINE) tool.

2011-12-16 12:54:21 -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

variant_detection

Fix inconsequential warning about when tag when loading FreeBayes.

2012-04-10 16:08:15 -04:00

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