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

Detect pdf files on upload [Brad Chapman]. Resolves #357

2010-07-02 18:10:45 -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

Next rev of codingSnps tool.

2010-03-24 14:14:58 -04:00

extract

Fix bug so that fasta identifier produced by 'extract genomic dna' tool for GFF files is consistent with GFF coordinates.

2010-07-15 17:03:14 -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

Fixed issue #345 - Incorporated Brad's patch which handles skipping of order checking for join version >=7, which would otherwise end in an error. Also modified sort command to better handle cases with duplicate keys. A new test-case to test these scenarios has been added as well.

2010-06-30 12:36:18 -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

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

Fixed functional tests for kcca, linear regression and get indels tools. Have used 're_match' to accommodate sign and decimal precision changes in kcca output.

2010-06-09 12:52:47 -04:00

new_operations

Update gops_intersect and gops_subtract documentation to reflect that tools can accept both BED and GFF files.

2010-08-04 14:04:37 -04:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Improvements to the GFF filtering tool.

2010-08-04 14:35:53 -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

Adding new regional variation tools developed by Zaky from Makova lab.

2010-04-27 15:36:55 -04:00

rgenetics

Fixes for rgManQQ - manhattan and qqplot generator for

2010-07-15 04:58:08 -04:00

samtools

Updating sam_indel_filter tool; adding NGS: Indel Analysis section; adding indel_analysis, indel_table, and indel_sam2interval tools

2010-07-14 01:09:52 -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

Make "loc files" more flexible by adding "tool data tables". These are

2010-07-08 14:36:59 -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