Greg Von Kuster
5dd014a91e
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
Greg Von Kuster
0f446b0568
Added Taxonomy manipulation tool section to main tool config.
2008-05-06 16:11:55 +00:00
Anton Nekrutenko
a3ee9be735
More clean up and modification of FASTA tools
2008-04-29 14:36:04 +00:00
Greg Von Kuster
67a4eac3d9
Added short read analysis tool section to tool_conf.xml.main
2008-04-28 20:01:48 +00:00
Greg Von Kuster
c0f960fe0c
Missed a sample locally cahced data file, added the Fetch closest feature tool to mains tool config.
2008-03-20 14:44:24 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +00:00
Greg Von Kuster
61903507e2
Enable changeCase tool on main.
2008-02-29 17:47:03 +00:00
Greg Von Kuster
335ebef0af
Restored version 1.1.0 of aggregate scores tool and moved the fixes to version 1.1.1.
2008-02-28 00:08:05 +00:00
Greg Von Kuster
9262212acd
Added tool version directories for validation and visualization tools directories.
2008-02-22 20:36:20 +00:00
Greg Von Kuster
78b2d4b78e
Added tool version directories for stats tools directory.
2008-02-22 20:26:57 +00:00
Greg Von Kuster
b75509fa17
Added tool version directories to regVariation tools directory.
2008-02-22 20:09:25 +00:00
Greg Von Kuster
218684f610
Added tool version directories for plotting tools directory.
2008-02-22 19:41:52 +00:00
Greg Von Kuster
99bc8db3fd
Added tool version directories to new_operations tools directory.
2008-02-22 19:23:18 +00:00
Greg Von Kuster
a2f475b55a
Added tool version directories for maf tool directory.
2008-02-22 18:35:01 +00:00
Greg Von Kuster
073d392616
Added tool version directories for hyphy tools, also added galaxy/tools/util directory to house utility code used acroos multiple tools.
2008-02-22 16:50:12 +00:00
Greg Von Kuster
b8599b819f
Finished adding tool version directories to filters tool directory.
2008-02-22 15:48:05 +00:00
Greg Von Kuster
32b40a5f27
Added more tool version directories for filters tool directoy.
2008-02-22 15:23:46 +00:00
Greg Von Kuster
37eeb64f61
Added tool version directory hierarchy for some tools in the filters tool directory.
2008-02-22 14:57:00 +00:00
Greg Von Kuster
dc554f04fa
Added tool version directory hierarchy for fasta_tools tool directory.
2008-02-22 14:31:30 +00:00
Greg Von Kuster
cabde35b99
Added tool version directory hierarchy for encode and extract tool directories.
2008-02-22 14:18:41 +00:00
Guruprasad Anada
82760a4c4b
Modified Lift-Over tool. The "TO" build-list will now be dynamically generated based on the input dataset's build.
2008-02-06 19:17:02 +00:00
Guruprasad Anada
407a287565
Modified Regional Variation section in tool_conf.xml.main. Commented out the Indel tools since I need to verify their outputs by running more tests with Erika.
2008-02-06 15:14:48 +00:00
Greg Von Kuster
d28623f203
Enabling EMBOSS 5.0.0 tools, cleaned up tool_conf.xml.sample and tool_conf.xml.main.
2008-01-29 18:45:21 +00:00
Greg Von Kuster
32ccd3570c
Fixes for tabular_to_fasta and fasta_to_tabular tools - requires update to datatype_converters_conf.xml
...
- Use ColumnListParameter rather than TextToolParameter
- Use better naming convertions for code and test-data files
- Added fasta_to_tabular converter to datatype_converters_conf.xml
- Fixed tool-conf so the converters are displayed in the Converters tool section
- Other miscellaneous cleanup.
2008-01-28 21:25:33 +00:00
Guruprasad Anada
0f7e0ea9be
Updated tool_conf.xml.main by adding dN/dS tool in HYPHY section.
2008-01-23 16:50:26 +00:00
Daniel Blankenberg
5b1552ffa8
Fix memory issues when dealing with MAF tools.
...
Add new bx-python eggs.
Reorganize all MAF tools into a unified directory, and update tool_conf.
Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
2008-01-16 18:01:09 +00:00
Greg Von Kuster
737bdf23f9
Enhanced upload to handle certain binary and zip files. Cleaned up the upload config. Added 4 new data types: ab1, scf, binseq.zip and txtseq.zip. Added Regional Variation section to tool_conf.xml.main.
2007-12-14 21:07:11 +00:00
Daniel Blankenberg
96afd6bf8d
Removing old/unused files for maf tools (mostly config files for user only versions).
2007-10-30 19:47:33 +00:00
Greg Von Kuster
3bce5b26be
Uncommented encode db tool for main.
2007-08-01 19:46:53 +00:00
Daniel Blankenberg
646a2ca7ac
MAF tools are no longer duplicated for different sources, i.e. locally cached and user histories.
...
Tests will not pass until testing framework is updated to be compatible with new tool options.
Several files can be removed, but have been left for the time being:
tools/filters/maf/maf_to_fasta_multiple_sets.xml
tools/filters/maf/maf_to_fasta_concat.xml
tools/extract/user_interval2maf.xml
tools/extract/interval_maf_to_merged_fasta_user.xml
tools/extract/interval_maf_to_merged_fasta_user_code.py
tools/extract/genebed_maf_to_fasta_user.xml
tools/extract/genebed_maf_to_fasta_user_code.py
2007-07-31 18:35:48 +00:00
Anton Nekrutenko
04561b1549
axt and lav converters are not needed in tool_conf.xml.main at the moment
2007-07-17 15:27:54 +00:00
Anton Nekrutenko
e130de1a26
More interface changes and updates to tool_conf.xml.main and tool_conf.xml.sample
2007-07-17 15:17:11 +00:00
Daniel Blankenberg
8bc14e03fa
Add a sample tool_conf file for the Main server, this file is called
...
'tool_conf.xml.main'.
tool_conf.xml.sample is used by the Testing frame work to determine which tools to
test, so it should have all tools undergoing testing.
2007-07-17 15:01:31 +00:00
Greg Von Kuster