Jeremy Goecks 0fddc97e94 Trackster: (a) refactor tool data functionality into TiledTrack class so that it is generally available; (b) enable VcfTracks to work with tools; and (c) more robust parameter setting. Enable Unified Genotyper to work with Trackster.

2011-11-01 10:49:34 -04:00

..

annotation_profiler

Tool help updates.

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

data_destination

merging from central

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

data_source

Some genomespace_file_browser tweaks.

2011-10-06 14:22:59 -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

FASTQ de-interlacer - fix for memory leak

2011-10-24 15:02:07 -05:00

fastx_toolkit

Minor tool help updates.

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

filters

Update sff extractor to version 0.2.10.

2011-10-20 16:38:14 -04:00

gatk

Trackster: (a) refactor tool data functionality into TiledTrack class so that it is generally available; (b) enable VcfTracks to work with tools; and (c) more robust parameter setting. Enable Unified Genotyper to work with Trackster.

2011-11-01 10:49:34 -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

Merge

2011-10-07 13:25:19 -07:00

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 typos.

2011-10-03 17:12:41 -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

Tweak validator for input bed file in SICER tool to work around workflow editor issue.

2011-10-03 11:11:16 -04:00

picard

GATK tools will now use gatk_picard_indexes data table.

2011-10-31 09:41:09 -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

Have Picard MergeSamFiles use return code to determine tool error.

2011-10-27 10:54:42 -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

Update SRMA wrapper to use data tables.

2011-10-31 09:49:51 -04:00

stats

Grouping tool: make error clearer when a line doesn't have entry on grouped column

2011-10-04 23:11:23 -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

…

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