Kelly Vincent f2aaa29988 Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options

2009-09-14 14:54:11 -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

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

Integration of Assaf Gordon's Solexa toolkit into Galaxy - (all tools except 3 are working fine).

2009-02-20 14:17:46 -05:00

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

Fix heading for Example 2 in maf_split_by_species onscreen tool help.

2009-09-04 11:08:10 -04:00

metag_tools

Fixed a stupid and truly horrible paired end splitter bug

2009-08-20 17:33:39 -04:00

new_operations

Bug fix for 'Fetch closest feature' tool.

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

next_gen_conversion

Renamed test files and fixed output datatype problem with solid-to-fastq tool

2009-08-04 16:32:57 -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

Added pileup parser. Pardon the perl = used to its regexes too much

2009-09-04 10:23:37 -04:00

solid_tools

Fixed a stupid and truly horrible paired end splitter bug

2009-08-20 17:33:39 -04:00

sr_mapping

Updated Bowtie wrapper tool to add a number of threads parameter and remove two unnecessary options

2009-09-14 14:54:11 -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