galaxy

annotation_profiler

Resync Annotation Profiler tests to current cached data.

2010-06-02 16:40:39 -04:00

data_destination

merging from central

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

data_source

Highlight the futility of uploading files >2GB via a browser.

2011-01-14 23:52:31 -05:00

discreteWavelet

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

emboss_5

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

encode

Fix gencode partition tool to not use hard-coded paths.

2009-12-09 15:21:41 -05:00

evolution

Fixes to aaChanges tool

2010-12-02 13:04:05 -05:00

extract

Move gff_util.py from galaxy/tools/util to galaxy/datatypes/util because gff_utils are now used by the framework as well as tools.

2010-11-14 11:29:44 -05:00

fasta_tools

Fix typo in fasta/fastq to tabular converters

2010-12-10 16:29:03 -05:00

fastq

Fix typo in fasta/fastq to tabular converters

2010-12-10 16:29:03 -05:00

fastx_toolkit

Allow fastx_toolkit clipper wrapper to work on fastqsanger formatted files.

2010-12-16 00:06:12 -05:00

filters

Bump wig_to_bigwig tool version

2011-01-04 19:49:44 -05:00

genetrack

Add bed6 and bed12 datatypes, which are subclasses of bedstrict; converters are available to turn any interval datatype into these types. Change GeneTrack Indexer tool and converter to use bed6 as input.

2010-04-01 13:08:48 -04:00

human_genome_variation

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -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

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

metag_tools

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

multivariate_stats

Added an option to perform PCA using prcomp()

2010-09-14 14:38:21 -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

Fix BLAST XML to tabular mismatch calculation when query is masked (with unit test based on failing example from Alex Bossers)

2010-11-24 15:05:08 +00:00

new_operations

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

next_gen_conversion

Updated output format for solid2fastq converter

2010-04-07 08:44:57 -04:00

ngs_rna

Update Cufflinks tool suite wrappers to support v0.9.3 and add support for bias correction to Cufflinks and Cuffdiff.

2011-01-03 11:25:03 -05:00

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

Change method of accessing additional fields by name for dynamically generated select lists which was added in 4784:7be369e7cc6f.

2011-01-05 14:57:05 -05:00

plotting

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -05:00

regVariation

Fixed a bug in microsatellite birth/death tool

2011-01-17 20:55:58 -05:00

rgenetics

Fixed edge case error handling when no matching rs

2011-01-15 21:06:17 +11:00

samtools

Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper

2011-01-12 13:31:04 -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

Convert a bunch of binary requirement tags to package requirements, and change the sputnik tool to call 'sputnik' instead of 'bx-sputnik'.

2010-10-07 16:23:57 -04:00

sr_mapping

Removed errant right parenthesis from BFAST wrapper command

2011-01-14 00:23:15 -05:00

stats

Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141

2010-12-14 14:22:13 -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

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

visualization

Create NGS peak calling section. Add MACS peak caller. Move GeneTrack to new section. Increment sam2interval tool version.

2010-02-05 16:06:27 -05:00