Daniel Blankenberg 401d95cc73 MAF stats tool will now skip intervals with length less 1.

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

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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

aaChanges tool: Added an option to keep the columns from the SNP dataset

2011-09-21 16:50:18 -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

Fix tabs in secure_hash_message_digest.xml.

2011-09-09 12:15:27 -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

New version of ctd.xml from Belinda (Human Genome Variation)

2011-09-21 11:36:58 -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 tool intefaces and help sections. Disabled java heap selection by the user (set to 4G default, which was changed in picard_wrapper.py).

2011-05-20 13:26:45 -04:00

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