Ross Lazarus 0a7d61f14f Fixes to picard HSmetrics and GCbias tools for warning message appearing in paster.log from a test parameter (maxmem) which ...

is available in the xml wrapper for sites wanting it but is commented out as distributed.
Simple solution now requires the test params to be uncommented too where sites want to expose the option

2011-09-27 14:37:17 +10:00

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annotation_profiler

Tool help updates.

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

data_destination

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data_source

Fix uploading sorted BAMs to libraries when using the link method rather than copying.

2011-08-26 15:59:29 -04:00

discreteWavelet

Update for wavelet variance tool contributed by Erika Kvikstad.

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

emboss_5

Tool help updates.

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

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

Minor tool help updates.

2011-08-25 10:00:09 -04:00

fastx_toolkit

Minor tool help updates.

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

filters

Some random lines tool tweaks.

2011-09-25 13:27:14 -04:00

gatk

Tool help updates.

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

genetrack

Tool help updates.

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

genome_diversity

updated error handling for genome diversity select snps tool

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

human_genome_variation

Fixed outstanding bugs in CTD tool (Human Genome Variation)

2011-09-26 15:56:01 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -05:00

ilmn_pacbio

Fix SOAPdenovo binary name

2011-08-26 10:39:34 -04:00

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

Fix bug in setting Cufflinks' reference annotation.

2011-09-02 08:57:55 -04:00

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.

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

picard

Fixes to picard HSmetrics and GCbias tools for warning message appearing in paster.log from a test parameter (maxmem) which

2011-09-27 14:37:17 +10:00

plotting

Minor tool help updates.

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

regVariation

Rounded the outputs of regression to 10 significant digits.

2011-06-27 15:44:59 -04:00

rgenetics

WebLogo3 wrapper repair to a string format edge case. Reports are good for finding these - user hadn't reported...

2011-08-20 14:27:30 +10:00

samtools

Update tests for samtools rmdup.

2011-09-01 09:38:16 -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

Import patch contributed by Assaf Gordon allowing bwa_wrapper to work directly on fastqillumina formatted files. Closes #635.

2011-08-08 09:35:48 -04:00

stats

Remove unspecified build validator from aggregate_scores_in_intervals2 tool because it can work with a custom fasta.

2011-08-24 14:38:29 -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

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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