Ross Lazarus 7d2dd59186 Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X. ...

Also cleaned up redundant file recreation - the code passes column numbers to R so the raw data can be read as supplied by Galaxy
Thanks to Alison Harrill for exposing some more input edge cases...

2011-07-20 12:17:43 +10:00

..

annotation_profiler

Update annotation profiler tool sample configuration file.

2011-07-07 12:13:49 -04:00

data_destination

merging from central

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

data_source

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

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

Typo

2011-06-10 13:15:17 -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

Patch from Peter Cock (bug534) for cut tool to ignore commented lines.

2011-06-08 17:17:11 -04:00

gatk

Have GATK file listings written as html, be sorted.

2011-05-12 12:13:18 -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

genome_diversity

updated error handling for genome diversity select snps tool

2011-06-17 12:16:53 -04:00

human_genome_variation

Updated Freebayes to set dbkey on output file

2011-05-09 16:40:44 -04:00

hyphy

Added functional test for hyphy NJ tree builder.

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

ilmn_pacbio

Add Pacific Biosciences tools.

2011-06-14 16:42:11 -04:00

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

Update tool help for some MAF tools.

2011-05-17 12:07:25 -04:00

meme

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

metag_tools

Improve BLAST parser tool error handling, and improve elementtree import as well.

2011-07-12 18:14:56 -04:00

multivariate_stats

Fixed a bug in PCA tool - standard deviation & prop variance values are now sorted by PC order.

2011-07-15 10:33:02 -04:00

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

Improve BLAST parser tool error handling, and improve elementtree import as well.

2011-07-12 18:14:56 -04:00

new_operations

Trackster improvements: (1) add trackster_conf tag to tool definition; for now, tag indicates that tool is compatible with trackster, but will have configuration information in the future; (2) use trackster_conf tag to indicate that Cufflinks, gops intersect, and gops subtract are compatible with Trackster; and (3) remove .track_type attribute and use of it and use instanceof operator instead.

2011-06-16 10:22:31 -04:00

next_gen_conversion

solid2fastq now correctly errors out for out-of-sync solid files. Adderesses user reported bug from yjx@rice.edu

2011-06-08 16:25:15 -04:00

ngs_rna

Rename version_string -> version_command, update wrappers

2011-07-12 17:04:16 -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

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

picard

Fixes to picard tool intefaces and help sections. Disabled java heap selection by the user (set to 4G default, which was changed in picard_wrapper.py).

2011-05-20 13:26:45 -04:00

plotting

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

regVariation

Rounded the outputs of regression to 10 significant digits.

2011-06-27 15:44:59 -04:00

rgenetics

Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.

2011-07-20 12:17:43 +10:00

samtools

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

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

Velvet wrapper: fix typos, tabs -> spaces, spacing

2011-05-27 11:01:46 +02:00

sr_mapping

Updated help section of BWA wrappers to include tags for the RG header record type

2011-05-12 13:38:00 -04:00

stats

Improve filtering tool's stdout reporting of lines filtered; fixes #536

2011-06-15 13:22:18 -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