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
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
Wen-Yu Chung
5b4e5a772b
modify data structure used in short read tools.
...
update functional test data.
2008-02-25 18:42:39 +00:00
Anton Nekrutenko
f607e77b6a
Tool for changing case
2008-02-25 15:15:18 +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
c2f5849504
Added tool version directories for metag_tools directory.
2008-02-22 18:44:05 +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
Wen-Yu Chung
f077afa436
update several xml files for better help descriptions.
...
modify section names and ids in tool_conf.xml.sample:
Fasta Tools -> FASTA manipulation
Metagenomics -> Short Read Analysis
remove short_reads_figure_length from tool_conf.xml.sample.
2008-02-05 18:32:42 +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
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- 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
Wen-Yu Chung
db325162ca
add version to the extract genomic dna tool.
2008-01-24 21:02:53 +00:00
Wen-Yu Chung
a33e647f11
add a section and tools for manipulating fasta file:
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convert file between fasta and tab format (should this be in section Convert Formats?);
filter fasta sequences by length;
compute lengths of fasta sequences.
add a megablast_wrapper, no functional test yet (maybe after we have designated machine?).
update extract_genomic_dna tool.
update tool_conf.xml.sample.
2008-01-22 16:45:35 +00:00
Wen-Yu Chung
45d34cc7b3
Update tools in metagenomics.
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Add one tool that deals with nib and 2bit file formats.
2008-01-21 17:49:54 +00:00
Wen-Yu Chung
7cb1467859
remove 2 tools that didn't pass functional test.
...
will update later.
2008-01-18 15:20:38 +00:00
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
Wen-Yu Chung
bd429b745e
forgot to update tool_conf.
2008-01-17 16:37:59 +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
Wen-Yu Chung
9f0f822deb
add a section: metagenomics
...
tools for running phred(need to change path later), trim sequence, generate boxplot and an array of length of the reads.
test data are added.
trim sequence and array of length passed functional test.
phred (2 ouput files) and boxplot (pdf file) didn't pass functional test yet.
2008-01-09 20:41:59 +00:00
Chinmay Rao
e59df6cff4
Config files reflecting updates of EMBOSS tools to v5.0
2007-12-17 17:01:23 +00:00
Guruprasad Anada
ab85984841
Adding tool "Get Indel rates for 3-way alignments" under Regional variation section.
2007-11-28 18:56:13 +00:00
Guruprasad Anada
71979fb76f
Added Feature coverage tool under Regional variation section. Also, cleaned up regVariation folder.
2007-11-26 15:36:33 +00:00
Guruprasad Anada
49bc4a4da4
Added Regional variation section to tool_conf.xml.sample.
2007-11-20 19:56:01 +00:00
Daniel Blankenberg
00c08ed340
Add a MAF Block Filter builder. Allows filtering based on chromosome and strand for selectable species.
2007-10-29 17:01:45 +00:00
Greg Von Kuster
ca2dfc6109
Better implementation of column restriction in subtract whole query tool. Eliminated old show_in_ucsc tool from tool_conf.xml.sample.
2007-08-07 13:17:51 +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
Daniel Blankenberg
c1647adb9c
Replacing archaea proxy with direction connection in tool_conf.xml.sample.
2007-07-18 15:25:48 +00:00
Daniel Blankenberg
39933d0ca3
Add MAF tools to reverse complement and to merge (thread) adjoining MAF blocks by
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species.
2007-07-17 18:51:32 +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
Daniel Blankenberg
3b55facf53
Re-adding the ucsc archea browser direct connection to the
...
tool_conf.xml.sample. since it was apparently removed and replaced with
the old proxy version in rev 1732.
2007-07-13 20:21:46 +00:00
Anton Nekrutenko
b4103b6649
Tool description cleanup. Next tool_conf. New logo
2007-07-13 18:36:44 +00:00
Guruprasad Anada
e75d088413
Forgot to add tool_conf.xml.sample. Also adding a small change to the tool code file.
2007-07-05 16:51:53 +00:00
Daniel Blankenberg
8e9b070fac
Add direct connection to ucsc archaea browser. We should no longer need the proxy.
2007-07-03 17:15:06 +00:00
Guruprasad Anada
4919d2d048
Adding new tool "Extract features from GFF file" under Fetch Sequences and Alignments section.
...
Have not been able to get this tool to pass functional test as test support with the new conditional constructs is yet to be worked out.
2007-06-19 14:04:41 +00:00
Guruprasad Anada
f59b70e1ae
Tool to extract genomic DNA from unassembled sequences.
...
Adding tool xml and code files, test data files and the twoBitToFa executable required by the tool.
2007-05-29 19:50:25 +00:00
Anton Nekrutenko
47d4764d1e
Forgot tool_conf -> new xy plot and custom track tools are enabled but lack tests
2007-05-25 20:41:15 +00:00
Ian Schenck
7c9f2f2c2e
removed final traces of baseml from tool_conf
2007-05-21 16:32:30 +00:00
Ian Schenck
6889b4380f
removed baseml from tool_conf
2007-05-21 16:28:18 +00:00
Greg Von Kuster