Nate Coraor ffd0be5a3a Merged from central.

2008-09-12 15:16:38 -04:00

..

annotation_profiler

More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.

2008-09-05 16:36:51 -04:00

data_source

Spiffy new library browser interface. Also, dim datasets in your

2008-09-10 10:10:13 -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

Fix for dataset_metadata_in_file validator: all locally cached data files that are columnar must have columns separated by tabs characters, not white space. I've eliminated the 'split' param from the validator as it was causing problems. Extract genomic DNA tool should now finally work correctly.

2008-08-22 11:22:44 -04:00

fasta_tools

Bug fix for Concatenate FASTA alignment by species tool.

2008-07-29 11:24:28 -04:00

filters

Fix functional test for count tool and correct spelling errors in template.

2008-09-08 09:16:32 -04:00

hyphy

Revert 2715.

2008-06-04 13:02:15 +00:00

maf

Better fix for interval_maf_to_merged_fasta when no strand column in input, added functional test.

2008-08-22 10:42:24 -04:00

metag_tools

Lastz with additional short read changes

2008-09-12 15:14:20 -04:00

new_operations

More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.

2008-09-05 16:36:51 -04:00

plotting

Fix for scatterplot.py: Handling an uncaught exception.

2008-09-08 14:36:37 -04:00

regVariation

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

sr_mapping

Lastz with additional short read changes

2008-09-12 15:14:20 -04:00

stats

Fix for grouping.py: New line character appended when grouping by the last column will now be trimmed.

2008-09-08 14:54:40 -04:00

taxonomy

typo

2008-07-07 15:17:32 +00:00

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

Update GMAJ tool to allow the specifying of annotations in two styles.

2008-09-08 16:00:49 -04:00