Daniel Blankenberg
1ebbc0c583
Fix for hyperlinks for UCSC table browser direct connection.
2007-03-08 16:35:58 +00:00
David C. King
078389e8f0
aggregate_binned_scores now invokes the up-to-date tool
2007-03-07 22:49:54 +00:00
Daniel Blankenberg
84e2dc5ed5
Fix for UCSC direct connection for unknown datatypes.
2007-03-01 16:22:29 +00:00
Daniel Blankenberg
e013dc254e
Make BED default datatype for UCSC direct connection.
2007-03-01 15:53:03 +00:00
Ian Schenck
bdb37ba8ce
Another change to ops to hopefully kill the never-ending strand problem. This makes anything that isn't a +/- into a +.
2007-02-28 21:59:38 +00:00
Daniel Blankenberg
412b9a9677
Add UCSC Table Browser direct connection tool.
2007-02-28 20:46:06 +00:00
Greg Von Kuster
0dfd869918
Enhanced column_maker.py to gracefully handle invalid data in input file and to display more meaningful info to user.
2007-02-28 16:10:31 +00:00
Greg Von Kuster
7ab5369033
Corrected the way these tools read input datasets to keep them from entering infinite loops if the dataset is empty.
2007-02-27 16:32:05 +00:00
Greg Von Kuster
0191564e9b
Added another example since I noticed several jobs where the user was confused about the "==" requirement.
2007-02-26 20:43:31 +00:00
Daniel Blankenberg
e830b83b9f
Removing import psyco_full from tools that throw warning (already imported).
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Also, I noticed that the 2 aggregate score tools had the same tool id, and are live on the test server, so i fixed the tool ids.
2007-02-23 14:33:03 +00:00
Greg Von Kuster
5a8135f56c
Minor correction to the message for the location of the first invalid line in a dataset, if there is in fact one.
2007-02-21 21:44:22 +00:00
Greg Von Kuster
67e1bb8846
Enhanced the Filter tool to handle invalid data and to display more useful, informative messages to the user.
2007-02-21 18:41:58 +00:00
Daniel Blankenberg
573e8cd8a2
Parameter sanitizer can now be turned off by individual tools. Refresh behavior after tool execution can now be defined in
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the tool xml file.
To Do: Allow individual parameters to have sanitation control.
2007-02-21 18:01:07 +00:00
Guruprasad Anada
9903924f97
Name change: Gene BED to Exon BED changed to Gene BED to Exon/Intron BED
2007-02-19 21:14:03 +00:00
Guruprasad Anada
84912a92fa
Filename test_kaks.py changed to kaks_yn00.py
2007-02-19 19:34:26 +00:00
Guruprasad Anada
be8f660cd3
yn00 binary added
2007-02-19 19:21:38 +00:00
Guruprasad Anada
ac747b8d6f
Modified tool: Gene BED to Exon BED
2007-02-19 16:59:51 +00:00
Guruprasad Anada
112f94c176
new tool: gene bed to intron bed
2007-02-19 16:22:28 +00:00
Guruprasad Anada
fb3b9255f5
yn00 binary added: kaks tool
2007-02-16 21:37:34 +00:00
Guruprasad Anada
b37f332a35
new toold kaks added
2007-02-16 21:28:21 +00:00
Daniel Blankenberg
bfe9c45db9
Modify maf_to_bed to use database/tmp for its temp directory for additional output files.
2007-02-15 20:09:33 +00:00
Anton Nekrutenko
e554fb4d79
added get_flanks plus two additional tools for a David Gilmore: srg2wig and aggTrack. These two are for demo only and should not go to main
2007-02-15 15:11:08 +00:00
Guruprasad Anada
02a60145bf
2007-02-13 17:01:13 +00:00
Guruprasad Anada
0ef3bdbba0
modified test_kaks tool
2007-02-13 16:21:07 +00:00
Guruprasad Anada
63a3bebef9
Added new tool: kaks (computes the ratio of nonsynonymous substitutions to synonymous substitutions for all the sequence alignments in the input
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file).
2007-02-12 21:38:36 +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
52b56c76eb
Build lists are now alphabetized (by display name) in edit attributes and the upload tool. More
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advanced grouping is not possible without additional outside information.
2007-02-05 18:50:07 +00:00
David C. King
ccb175927b
score aggregate tool for .wig files
2007-01-22 20:28:36 +00:00
Ian Schenck
59f764fe84
This should catch parse errors, which are errors with bad lines in interval files, such as bad strands or generally malformed lines. The message is a little more human readable, and I expect to improve this.
2007-01-17 20:41:52 +00:00
Yi Zhang
afe64697df
old changes copied to trunk: descriptions of 'Edit Queries' tools
2007-01-17 19:00:33 +00:00
Yi Zhang
d418956bf9
old changes copied to trunk: description of tool 'Compute'
2007-01-17 18:55:46 +00:00
Daniel Blankenberg
624037d52c
Fix aggregate binned scores in intervals. This tool could definitly use more friendly error messages.
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misc module provided a method for opening and guessing the type of a compressed file by
extention. Does not appear that the module was even used.
2007-01-16 17:36:00 +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
fc40c7f3d6
Fix help link for all EMBOSS tools.
2007-01-11 16:47:46 +00:00
Daniel Blankenberg
8554c031ed
Push Microbial datasource changes onto trunk.
2007-01-10 15:23:30 +00:00
Nate Coraor
8f8dd92373
Remove last references to /depot/data1/cache.
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All binned scores moved to scofield:/cache, chrominfo.txt is copied
nightly from herbie via a cron job. This can go away when galaxyOps is
no longer in use.
2007-01-03 19:36:07 +00:00
Daniel Blankenberg
97c1ac33f7
Some items that were not copied over to trunk.
2006-12-21 00:14:11 +00:00
Anton Nekrutenko
c879bae96f
TRUNK:More fixes for uniq and STDERR printout
2006-12-20 19:15:54 +00:00
Anton Nekrutenko
90fe4385d1
TRUNK:a Typo
2006-12-20 02:52:00 +00:00
Anton Nekrutenko
c16dc08e00
TRUNK:More cut changes
2006-12-20 02:44:02 +00:00
Anton Nekrutenko
b840959a1c
TRUNK:This trunk/brunch stuff is VERY confusing. Again: Fix for uniq (count). No more leading spaces
2006-12-20 01:53:04 +00:00
Anton Nekrutenko
37d815d298
Trunk:Fix for uniq (count). No more leading spaces
2006-12-20 01:26:58 +00:00
Anton Nekrutenko
cea78e73f7
Fix for uniq (count). No more leading spaces
2006-12-20 01:23:07 +00:00
Anton Nekrutenko
73b53ba17c
for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets
2006-12-18 21:35:43 +00:00
Anton Nekrutenko
32106fd6d5
cut for trunk
2006-12-18 18:38:37 +00:00
Daniel Blankenberg
9d1dd9fb51
Biomart: add chr to the front of X and Y when in the chrom column.
2006-12-18 16:52:33 +00:00
Daniel Blankenberg
c198156ee3
Add 'URL' to the list of parameters that are not sanitized. URL is used for datasources such as biomart (and hbvar soon).
2006-12-15 19:10:00 +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
Daniel Blankenberg