Jeremy Goecks 23a8b191a7 Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.

2011-02-10 17:19:40 -05:00

..

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 metabolicMine datasource tool.

2011-02-09 15:42:42 -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

Extend extract_genomic_dna tool to support GFF/GTF features and custom genomes. For GFF/GTF files, tool provides option to return sequence data for each feature's intervals, which are split across lines in GFF/GTF files. Tool also now accepts sequence data from a history item, enabling the extraction of data from custom genomes. New functional tests added to cover new functionality.

2011-02-10 17:19:40 -05:00

fasta_tools

Fix typo in fasta/fastq to tabular converters

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

fastq

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

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

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

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -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

meme

Add MEME tool configuration file.

2011-02-01 11:17:44 -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

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -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

Avoid using shell=True when we call subprocess to ensure if the Python script is killed, so too is the BLAST process

2011-02-01 15:24:45 +00:00

new_operations

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

next_gen_conversion

Updated output format for solid2fastq converter

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

ngs_rna

Enable Cuffcompare to take an arbitrary number of input GTFs. However, the wrapper does not currently keep track of all outputs tmap and refmap files because Galaxy cannot generate output files corresponding to each input.

2011-01-28 16:28:12 -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

Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson.

2011-02-03 15:52:44 -05:00

regVariation

Better handling of complex interrupted microsatellites in 'Extract orthologous microsatellites for multiple species alignments' tool.

2011-02-10 10:33:08 -05:00

rgenetics

First pass standardizing to 'dataaset' from 'query'.

2011-01-27 13:46:20 -05:00

samtools

Change output format of samtools flagstat from 'text' to 'txt'.

2011-01-26 15:45:27 -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

Fixed ValueError being thrown by randint() function in group tool.

2011-01-28 10:42:08 -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