Dave Clements 9d0e631203 Updated "Example" images shown at the bottom of many ...

"Operate on Genomic Invervals" tool pages.  Old onew were looking dated.
New ones look, well, newer, and cover more cases.

2011-12-19 02:44:31 -08:00

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annotation_profiler

Add information for UCSC data to annotation profiler.

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

data_destination

merging from central

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

data_source

Update EBI SRA tool's input action.

2011-12-14 09:37:45 -05:00

discreteWavelet

Update for wavelet variance tool contributed by Erika Kvikstad.

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

emboss_5

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

encode

Tool help updates.

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

evolution

python version of "phyloP interspecies conservation scores" tool

2011-11-30 12:05:59 -05:00

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

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

Update GATK tools handling annotations to allow manually specifying additional annotation names to apply.

2011-12-06 09:42:56 -05:00

genetrack

Update GeneTrack help.

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

genome_diversity

updated error handling for genome diversity select snps tool

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

human_genome_variation

"Convert CG MasterVar file to pgSnp format" tool and test data

2011-11-28 13:15:08 -05:00

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

Have fimo.xml use fields.path approach instead of directly filtering on data table.

2011-11-22 12:21:05 -05:00

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

Improve BLAST parser tool error handling, and improve elementtree import as well.

2011-07-12 18:14:56 -04:00

new_operations

Updated "Example" images shown at the bottom of many

2011-12-19 02:44:31 -08:00

next_gen_conversion

Update links to reflect Galaxy Wiki moving away from Bitbucket.

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

ngs_rna

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

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

picard

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

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

Fixes for the new horrible FastQC html layout. Now wastes a whole lot of space on the left

2011-11-16 07:34:51 +11:00

samtools

The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.

2011-12-06 11:42:12 -05:00

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

Minor fix for 04e8ed0cd930.

2011-11-29 17:35:14 -05:00

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

…

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