Ian Schenck
77f1195f7a
Changed trans->app.
2007-05-31 20:31:28 +00:00
Ian Schenck
be673c2a5a
There has to be at least one tool named 'ucsc_proxy' for the proxies to work. They all use the same code with different urls, but they have to submit back to the tool_runner at the end. This closes ticket 121.
2007-05-30 15:47:59 +00:00
Ian Schenck
7b5aa376e9
Fix for microbial data. get_html_param_map wasn't able to pass the context of the inputs into the page, which was crashing things.
2007-05-24 18:36:28 +00:00
Daniel Blankenberg
410a9641b8
More friendly error message for when ucsc table browser is down.
2007-05-23 14:45:38 +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
Greg Von Kuster
401e30e2c5
Requires db schema change. Enhance upload tool to default to the last build used in the "current" history.
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Database changes required:
alter table history add genome_build varchar(40);
There is now a new tool ToolParameter named GenomeBuildParameter which should be useful in several existing tools.
Also took care of some other miscellaneous items.
2007-04-19 20:53:16 +00:00
Guruprasad Anada
192f2af527
Made necessary modifications to /lib/galaxy/tools/__init__.py and added the test input and output files for "Display customtrack at UCSC" tool.
2007-04-13 15:58:39 +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
Greg Von Kuster
e34fff8ff8
Added a corner-case fix for auto-detect file formats. Updated info displayed to user on upload and filter tools and added more valid words to filter tool.
2007-03-23 17:46:06 +00:00
Daniel Blankenberg
ad8719b852
Fix ucsc test browser.
2007-03-21 19:59:58 +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
3345e2b3a0
Added new tool: Display in UCSC.
2007-03-20 19:39:29 +00:00
Greg Von Kuster
9a4e8dc19c
Integrated Belinda's hbvar data source. The functional test fails, but Jianbin will look at it.
2007-03-16 15:22:28 +00:00
Nate Coraor
7ac51f24fc
All of the stuff in /cache has been moved to /depot/data2.
2007-03-13 21:27:39 +00:00
Daniel Blankenberg
5f67a58a9b
Add customtrack datatype. This is a skeleton class for now, allows viewing at ucsc and formatted
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peeking.
2007-03-09 21:28:09 +00:00
Daniel Blankenberg
d389d70b5b
Add sequence to tablebrowser direct connection. Custom track can be added after an actual datatype is created.
2007-03-08 16:42:48 +00:00
Daniel Blankenberg
1ebbc0c583
Fix for hyperlinks for UCSC table browser direct connection.
2007-03-08 16:35:58 +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
Daniel Blankenberg
412b9a9677
Add UCSC Table Browser direct connection tool.
2007-02-28 20:46:06 +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
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
Daniel Blankenberg
8554c031ed
Push Microbial datasource changes onto trunk.
2007-01-10 15:23:30 +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
Ian Schenck