Guruprasad Anada edd8093627 Commenting out functional test for fastx_collapser tool as the order of sequences in the output seems to differ between 32 bit and 64 bit machines.

2009-09-18 15:48:06 -04:00

..

annotation_profiler

removing debuging statements from annotation_profiler that were never inteded to go out

2009-09-04 10:49:02 -04:00

data_destination

merging from central

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

data_source

Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally

2009-09-10 14:52:38 -04:00

emboss_5

Forgot to eliminate the emboss path...

2008-04-25 19:07:26 +00:00

encode

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00

evolution

Add a new tool, Mutate by SNP codon, which will take codon position and sequence information that is joined to SNP data and create a 'mutated codon'.

2009-09-15 12:04:14 -04:00

extract

Change dbkey of unmapped liftover dataset to the input dataset's dbkey.

2009-08-21 11:40:51 -04:00

fasta_tools

Fixed for functional tests for new version of fasta_filter_by_length tool contributed by James Casbon.

2009-07-23 14:31:11 -04:00

fastx_toolkit

Commenting out functional test for fastx_collapser tool as the order of sequences in the output seems to differ between 32 bit and 64 bit machines.

2009-09-18 15:48:06 -04:00

filters

Testing framework will now click the add button for nested repeats when repeat content has been specfied.

2009-08-05 11:54:34 -04:00

hyphy

Fixes to get functional tests working.

2009-02-03 18:34:27 -05:00

maf

Add a MAF to Interval converter that produces a set of intervals with sequence data.

2009-09-17 11:47:37 -04:00

metag_tools

small tweaks

2009-09-18 11:11:41 -04:00

new_operations

Bug fix for 'Fetch closest feature' tool.

2009-09-10 17:35:21 -04:00

next_gen_conversion

Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool.

2009-09-18 12:11:43 -04:00

plotting

Fix bar chart output format.

2009-08-03 16:38:27 -04:00

regVariation

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

samtools

First pass of consolidating NGS tools

2009-09-18 10:27:03 -04:00

solid_tools

Adding qualsolid_boxplot_graph.sh script used by SOLiD quality boxplot tool to the distribution.

2009-09-18 14:21:59 -04:00

sr_mapping

Added header removal option to BWA wrapper tool, and cleaned up its test files. Also added the bwa_solid2fastq_modified.pl script to the next gen conversion directory for the solid-to-fastq tool.

2009-09-18 12:11:43 -04:00

stats

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00

taxonomy

Fixed finf_diag_hits plus a ttypo correction

2009-04-21 09:36:42 -04:00

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

Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.

2009-08-14 15:37:31 -04:00