Gert Hulselmans fb01c3cc96 Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool. ...

Add an option in the upload tool to disable the conversion of universal
line endings to Posix line endings.
This is useful for avoiding corruption of uploaded files when a binary
file is contained inside a gzip, bz2 and zip archive.

This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702

2013-05-27 20:55:52 +02:00

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annotation_profiler

Add information for UCSC data to annotation profiler.

2011-11-16 10:40:55 -05:00

data_destination

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data_source

Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.

2013-05-27 20:55:52 +02:00

discreteWavelet

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

encode

Tool help updates.

2011-09-21 04:11:07 -04:00

evolution

Make wrapper compatible with python 2.5.

2013-01-23 12:32:05 -05:00

extract

Replaced "query" with "dataset" in a number of tool definition XML files.

2013-01-14 16:13:54 -08:00

fasta_tools

Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.

2012-03-08 11:09:14 -05:00

fastq

tool tip fix for fastq summary and sorter

2013-03-19 11:50:03 -04:00

fastx_toolkit

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

filters

grep/select tool: fixed tab-delimiter matching for GNU version of grep

2013-04-02 15:18:22 -04:00

gatk

Covert more duplicated GATK wrapper code to macros.

2013-03-22 00:41:08 -05:00

genetrack

Update GeneTrack help.

2011-11-10 11:54:50 -05:00

genomespace

Update GenomeSpace tools to use __user__ as needed.

2013-05-03 16:02:40 -04:00

hyphy

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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

Make maf-to-bed object-store aware

2013-03-06 12:40:31 -05:00

meme

Specify meme requirement for fimo tool.

2012-02-02 21:29:30 -06:00

metag_tools

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -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

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

new_operations

Subtract query tool: make ignoring empty end columns and whitespace optional.

2013-02-07 14:46:49 -05:00

next_gen_conversion

Fixed error in solid2fasta.xml preventing help text from displaying.

2012-09-04 10:15:18 -04:00

ngs_rna

Add library normalization and dispersion options to Cuffdiff wrapper.

2013-05-19 11:59:50 -04:00

ngs_simulation

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

peak_calling

Tool help updates.

2011-11-14 13:26:29 -05:00

phenotype_association

Update functional test parameters so tests will pass.

2013-01-22 15:54:49 -05:00

plotting

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

regVariation

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

rgenetics

Remove unused test parameter.

2013-01-14 14:00:21 -05:00

samtools

Require pileup format as input to pileup parser tool.

2012-08-23 15:58:11 -04:00

solid_tools

Fix tool tip for compute quality statistics

2013-03-19 12:04:24 -04:00

sr_assembly

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

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

sr_mapping

Change order of Bowtie2 output datasets to put aligned reads at top of history.

2013-01-30 12:55:49 -05:00

stats

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

taxonomy

Use mako template in tool help so that dynamic image paths can be used. Fixes #141

2012-08-07 09:40:51 -04:00

validation

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vcf_tools

Fix for vcf_extract tool test

2011-03-02 09:40:10 -05:00

visualization

Performance enhancements for Build custom track for UCSC genome browser tool.

2012-10-16 15:25:01 -04:00