Wen-Yu Chung
9f0f822deb
add a section: metagenomics
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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.
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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
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'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
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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.
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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.
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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
Daniel Blankenberg
f8b0ab3f88
Add pairwise maf extractor for converted AXTs, add
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interval_to_maf_merged, and a whole bunch of MAF updates.
2007-05-16 18:42:34 +00:00
Jianbin He
cd18224159
switch findcluster tool from postgres to mysql
2007-05-14 14:24:18 +00:00
Greg Von Kuster
5b345d0b4c
Changed behavior of history import and added BioMart test instance.
2007-05-11 13:06:30 +00:00
Greg Von Kuster
39f811eff7
Added new Subtract Whole Query tool. Also some miscellaneous code clean-up.
2007-05-07 18:59:15 +00:00
Jianbin He
f2bf096005
add a new section and a new tool, find-cluster
2007-04-13 21:08:22 +00:00
Guruprasad Anada
012e460482
Adding tool "Display customtracks at UCSC" under Graph/Display data tab. I've added new param attributes called repeat (to repeat the param a certain number of times) and condition (to display or not display the param) and have added dynamic_options for type "data" in order to facilitate multiple data selection. These changes required certain modifications in the framework (/lib/galaxy/tools/__init__.py and parameters.py , /lib/galaxy/datatypes/interval.py and in templates/tool_form.tmpl). I ran functional tests and found no errors in any of the tools due to these modifications. There were the usual assertion errors and database errors.
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Modified get_flanks.py and get_flanks.xml files. Better exception handling and tool tips.
Also moved GMAJ and LAJ tools to Graph/Display data section.
2007-04-12 16:52:39 +00:00
Daniel Blankenberg
027b85f612
Add Gene bed and maf to fasta tool.
2007-04-10 16:11:04 +00:00
Daniel Blankenberg
3b0852ee01
Add a tool to select maf blocks by number.
2007-04-05 18:26:44 +00:00
Daniel Blankenberg
fe136cdefa
Add tool to compute maf alignment coverage.
2007-04-05 17:57:16 +00:00
Daniel Blankenberg
6d7d82cd93
Add a tool to allow filtering by MAF block size.
2007-04-05 14:55:05 +00:00
Daniel Blankenberg
5f1b12b56e
Add neighbor joining tree building via HYPHY.
2007-04-04 15:44:37 +00:00
Guruprasad Anada
c2c485ad48
Changes made in get_flanks tool and the revised .py, .xml, test data and tool_conf.xml.sample files are being committed.
2007-03-27 17:12:58 +00:00
Daniel Blankenberg
8a207dcd87
Update UCSC direct connection to use main ucsc site. Add direct test
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connection.
2007-03-21 19:52:01 +00:00
Nate Coraor
b6c07724fe
Reverting changes back to 1479 per Greg.
2007-03-21 15:06:34 +00:00
Guruprasad Anada
3462a49ae4
Updated tool_conf.xml.sample: Renamed Graph data tab as Plot/Display data and included Display in UCSC, GMAJ and LAJ tools under it.
2007-03-20 21:56:32 +00:00
Guruprasad Anada
bf1a7e38cc
Updated tool_conf.xml.sample with a link to the new tool Display in UCSC under Get Data tab.
2007-03-20 20:14:56 +00:00
Greg Von Kuster
2b05ca975f
Fixed a bug in sniff.py and added a new unit test case to cover it. Added the hpvar data source tool to tool_conf.xml.sample. Slightly enhanced the filter and compute tools.
2007-03-19 19:55:57 +00:00
Daniel Blankenberg
005a444f9c
Add HYPHY branch lengths tool.
2007-03-13 18:23:08 +00:00
Ian Schenck
fda163bbe8
Data validation. Please please please take a look and give me some input.
2007-03-12 18:35:03 +00:00
Daniel Blankenberg
412b9a9677
Add UCSC Table Browser direct connection tool.
2007-02-28 20:46:06 +00:00
Guruprasad Anada
583e91610d
new tool added: kaks
2007-02-12 22:03:06 +00:00
Daniel Blankenberg
0177cd59cc
Add tool to allow users to limit a MAF to a set of species.
2007-02-08 21:24:39 +00:00
Daniel Blankenberg
547ecf0960
Removing arch and module directories. Removing old operations (and tests), since they require arch; updated tool_conf.xml.sample.
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Removed non-arch specific cheetah egg, since compiled c code (once located in arch) is included in arch specific eggs. Removed a
tool called basicStats2, which used arch, but hasn't been in tool_conf.xml for some time.
2007-01-16 17:05:33 +00:00
Daniel Blankenberg
a7c848eb22
AXT to LAV does work.
2006-12-14 21:22:47 +00:00
Daniel Blankenberg
74784e1755
Pushing my changes from james-wsgi branch onto the trunk.
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Biomart doesn't work on the trunk yet (Before or after this commit).
axt to lav tool won't be functional until multiple datasets per history item is available on trunk - although I could
make it so that only the lav file is generated and no fasta files, in which case it wouldn't be an issue.
2006-12-14 21:02:17 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Wen-Yu Chung