Guruprasad Anada 987e2c7c4e Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.

2008-01-17 19:24:34 +00:00

..

data_source

Added blurb to Get ENCODE Data tools telling user data may not be current.

2008-01-14 21:39:11 +00:00

emboss

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

emboss_5

Committing EMBOSS v5.0 tools tcode textsearch tmap twofeat vectorstrip wordmatch with associated functional test files

2007-12-17 14:38:16 +00:00

encode

New reports app server and 1st report showing disk usage for dataset file system - still need to mess with styles a bit.

2008-01-11 21:24:21 +00:00

extract

Adding liftOver tool. Test section is commented as the functinal test module doesn't handle multiple outputs yet. I've downloaded liftOver mapping files from UCSC for all the genomes for which we have sequences. I've added a function in get_ucsc_scores.pl file (which contains functions to fetch sequences and alignments) to fetch liftOver mappings too.

2008-01-17 19:24:34 +00:00

filters

Fix memory issues when dealing with MAF tools.

2008-01-16 18:01:09 +00:00

hyphy

Adding HYPHY tool to compute dN/dS ratio.

2007-07-11 20:05:20 +00:00

maf

Missed something with MAF tools.

2008-01-16 18:09:37 +00:00

metag_tools

remove a tool that require phred.

2008-01-17 16:36:07 +00:00

new_operations

Reverting the test data for the gops_cluster tool to that which was originally used by Ian in rev 1636.

2008-01-07 13:02:10 +00:00

patmat

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

plotting

Bug fix in histogram tool.

2007-12-11 21:41:31 +00:00

regVariation

Uncommented functional tests in some regVariation tools in preparation for moving them to main.

2007-11-30 13:43:59 +00:00

stats

Better way to skip invalid comment lines in filtering tool. Better numerical value checks in interval.py.

2007-12-18 14:52:04 +00:00

validation

Cleanup: removing the cookbook package. Bunch and odict move to galaxy.util, tools

2007-07-31 15:45:59 +00:00

visualization

Eliminated Dataset.state.FAKE (requires db update), replacing it with Dataset.state.OK since fake datasets are removed, causing problems for workflow.

2007-12-21 19:31:58 +00:00