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 a new "Files uploaded via FTP" grid to the upload form and related parameter types, form fields, etc.

2010-11-05 11:04:50 -04:00

discreteWavelet

Adding wavelet analysis tools made by Zaky from Makova lab.

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

emboss_5

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

encode

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

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

evolution

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

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

fasta-to-tabular tool now adds a newline at the end. Closes #385

2010-09-24 16:49:16 -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 interpreter for the FASTX Barcode Splitter.

2010-11-04 16:25:51 -04:00

filters

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

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

updates to DAVID, LPS, and formatHelp help text

2010-10-05 11:59:36 -04:00

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

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

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

metag_tools

Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.

2010-11-08 00:10:13 -05:00

multivariate_stats

Added an option to perform PCA using prcomp()

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

mutation

mutation viz tool UI fixes

2010-10-22 11:30:03 -04:00

ncbi_blast_plus

Remove broken blastn test

2010-10-25 11:07:43 +01:00

new_operations

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

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Update Tophat and Cufflinks tool wrappers and functional tests to support Tophat version 1.1.* This breaks support for Tophat versions 1.0.* and earlier.

2010-11-08 15:21:34 -05:00

ngs_simulation

Corrected bug in reference to genome file in NGS simulation tool

2010-11-11 11:29:31 -05:00

peak_calling

Add descriptive labels to output dataset names for MACS peakcalling tool.

2010-10-19 13:13:55 -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

Actually change the invocation of sputnik from bx-sputnik as mentioned in my last commit. Thanks Kanwei.

2010-10-07 16:50:37 -04:00

rgenetics

rgHaploView tool version upgrade - now shows thumbnail of ld plots

2010-11-09 12:12:32 -05:00

samtools

Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria

2010-11-13 14:37:26 -05:00

solid_tools

Fix solid_qual_stats tool when value is 0 or not a valid int. Fixes #405

2010-10-26 13:46:03 -04:00

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

Minimally functional splitting.

2010-11-10 12:06:05 -05:00

stats

Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.

2010-11-04 16:30:34 -04:00

taxonomy

Changing back

2010-11-15 15:06:41 -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