Daniel Blankenberg 377c2427a7 Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode. ...

Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size.

The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.

2009-02-04 14:55:45 -05:00

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annotation_profiler

Fix annotation profiler interpreter to be python, not python2.4

2009-01-30 11:37:51 -05:00

data_destination

merging from central

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

data_source

merging from central

2009-01-22 08:51:48 -05:00

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

Added Validator to a bunch of tools..

2008-10-17 13:02:26 -04:00

fasta_tools

remove the usage of hast tables in the fasta-tools

2009-01-19 15:47:02 -05:00

filters

Bug fixes for compare, Group and filter tools.

2008-12-02 11:41:25 -05:00

hyphy

Fixes to get functional tests working.

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

maf

Allow workflows that contain tools that had parameters added to them after the workflow was created to be edited. Workflows containing tools with added parameters can still not be run until after they are edited and saved. Default values are provided in the workflow building mode.

2009-02-04 14:55:45 -05:00

metag_tools

Add support for NCBI Blast XML data format.

2009-01-07 12:20:35 -05:00

new_operations

Added more test-cases to GOPS JOIN to include cases with different cut-offs for overlap.

2008-12-12 12:12:59 -05:00

plotting

updated bar charter to use png instead of pdf

2009-01-22 12:06:29 -05:00

regVariation

Fixes to get functional tests working.

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

sr_mapping

Finally remerged changeset. Should be good now.

2009-01-21 16:48:54 -05:00

stats

Adding modified hyphy functional test output files, which have changed as the new version of HYPHY is installed on Galaxy. Also changing version numbers for all the affected tools.

2009-01-27 16:17:22 -05:00

taxonomy

Lca commit. The tool itself is written by guru with minor modification made by me.

2009-01-21 09:51:06 -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

visualization

Ironed out nasty exceptions thrown on invalid genetrack outputs. Still need a way to resolve the optional 2nd output (exported intervals), and ensure the user picks at least 1 coverage dataset or 1 feature dataset.

2009-01-27 17:10:30 -05:00