galaxy

2011-04-13 21:02:06 +02:00

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

Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.

2011-04-21 13:12:10 -04:00

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

Fix bug in extract_genomic_dna to handle non-GFF files when interpret features is true. Tweak functional test to cover new behavior.

2011-02-16 21:46:23 -05:00

fasta_tools

Fix typo in fasta/fastq to tabular converters

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

fastq

Add more verbose error reporting to FASTQ Groomer tool.

2011-03-24 11:45:50 -04:00

fastx_toolkit

Update FASTX tool wrappers to handle fastqsanger by passing -Q 33 to command-line as needed.

2011-01-27 09:54:53 -05:00

filters

Fix bug in 'Filter GTF data by attribute values list' tool.

2011-05-03 09:45:40 -04:00

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

genome_diversity

initial version of Webb's genome diversity tools

2011-04-21 17:22:27 -04:00

human_genome_variation

fixed some configuration files

2011-04-13 21:02:06 +02:00

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

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

meme

Update test-data files for meme 4.6.0

2011-02-25 14:58:35 -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

An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.

2011-03-08 11:17:57 -05:00

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

BLAST+ HTML output test

2011-04-19 16:20:52 +01:00

new_operations

Make gops subtract tool compatible with GFF features rather than lines.

2011-05-03 11:35:21 -04:00

next_gen_conversion

Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.

2011-02-28 12:16:28 -05:00

ngs_rna

Add unspecified build validators to dataset inputs for Cufflinks/compare/diff wrappers.

2011-05-03 10:31:14 -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

Update CCAT to version 3.0.

2011-03-16 10:41:38 -04:00

picard

second test for picard asmetrics fails on buildbot. This fix works on my own testbed - but then, it worked before too...

2011-04-29 17:32:33 -04:00

plotting

An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.

2011-03-08 11:17:57 -05:00

regVariation

An uninitialized value in R's PDF driver was causing it to sometimes randomly add a few elements to PDF outputs. The bug has been fixed in the buildbot environment and these changes account for that fix.

2011-03-08 11:17:57 -05:00

rgenetics

fix for missing html ref in picard_reordersam and for data index srma_indexes in gcbias

2011-04-28 16:25:09 -04:00

samtools

Enhance BAM to SAM tool to optionally output headers.

2011-04-18 16:41:51 -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

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

Set the ftype of SRMA test outputs so the BAMs are compared as SAMs

2011-03-23 10:59:26 -04:00

stats

Update help and description for Draw ROC plot tool. Questions and comments should be directed to Chungoo Park.

2011-04-15 13:55:45 -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

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

vcf_tools

Fix for vcf_extract tool test

2011-03-02 09:40:10 -05:00

visualization

fixed some configuration files

2011-04-13 21:02:06 +02:00