Jeremy Goecks 2d5b74aa6d Set Cufflinks global model when upper quartile normalization is used.

2011-12-22 13:54:33 -05:00

..

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

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

Set Cufflinks global model when upper quartile normalization is used.

2011-12-22 13:54:33 -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