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

Add support for bz2 compressed uploads.

2010-09-10 14:07:16 -04:00

discreteWavelet

Adding wavelet analysis tools made by Zaky from Makova lab.

2010-08-16 18:30:37 -04:00

emboss_5

Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .

2009-12-07 10:19:41 -05:00

encode

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

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

evolution

Initial checkin of Human Genome Variation tools

2010-09-14 18:20:15 -04:00

extract

Fix filenames problem in 'extract genomic dna' GFF functional tests that was introduced in 4200:291183d3896b .

2010-09-01 09:10:58 -04:00

fasta_tools

Sync hashbangs

2010-04-01 20:36:31 -04:00

fastq

Enhance Tool Repeat Grouping parameter to allow specifying min, max, and default repeat unit counts.

2010-07-14 12:15:14 -04:00

fastx_toolkit

Fix accidentally committed fastx tool configs

2010-01-07 16:20:04 -05:00

filters

Fix for tools/filters/wig_to_bigwig.xml when coordinates extend beyond chromosome boundaries and -clip was specified.

2010-09-01 19:26:25 -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

human_genome_variation

made BEAM wrapper more portable

2010-09-17 14:23:55 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

2010-02-04 11:56:58 -05:00

indels

Updated indel analysis tools: fixed counting bugs in indel_analysis and improved help section; standardized CIGAR regex across tools; updated test files for several tools

2010-07-21 16:25:46 -04:00

maf

Automated merge with https://bitbucket.org/galaxy/galaxy-central/

2010-08-04 14:01:39 -04:00

metag_tools

Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani.

2010-06-23 16:48:13 -04:00

multivariate_stats

Added an option to perform PCA using prcomp()

2010-09-14 14:38:21 -04:00

mutation

removed print stmts

2010-09-20 12:52:37 -04:00

new_operations

Fixed another bug in column join so it will handle filling empty columns properly

2010-08-20 17:04:16 -04:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Do not use unsanitized parameter in tophat wrapper.

2010-09-13 21:53:36 -04:00

peak_calling

Add eland and elandmulti formats. Enhance MACs peakcaller to properly handle these formats.

2010-04-27 10:59:46 -04:00

plotting

Make boxplot tool respect exit codes when determining job errors: makes e.g. 'Could not find/open font when opening font "arial", using internal non-scalable font' a non-fatal warning. Add version attribute to gnuplot requirement tag.

2010-03-22 11:06:40 -04:00

regVariation

Fix typo in Compute Motifs Frequency tool blurb.

2010-09-03 13:39:21 -04:00

rgenetics

rgManQQ changes - for some reason ggplot2 was really slow and timeed out on testing!!

2010-09-18 20:59:40 -04:00

samtools

Added BAM-to-SAM tool

2010-09-01 09:44:12 -04:00

solid_tools

Remove obsolete binseq.zip and txtseq.zip formats, and allow for uploading single files in a zip archive. Adapted from a patch from Pablo Cingolani.

2010-06-23 16:48:13 -04:00

sr_assembly

Add support for velvet data types and velveth and velvetg tool wrappers, all contributed by James E Johnson - University of Minnesota.

2010-06-09 11:23:10 -04:00

sr_mapping

Don't use unsanitized parameters in BWA, Bowtie, and PerM wrappers

2010-09-16 11:19:08 -04:00

stats

Modified Group tool by adding Mode function to the list of aggregate operations.

2010-07-29 12:21:09 -04:00

taxonomy

Bug fixes to LCA tool

2010-02-22 16:22:12 -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