Greg Von Kuster
79745f4012
Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py.
2007-11-29 17:04:42 +00:00
Greg Von Kuster
300d66fb11
Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.
2007-11-21 18:48:37 +00:00
Greg Von Kuster
e190e6e2b0
Enhancements to the way dynamic_options work in order to enable tools using dynemic_options to function in workdflow.
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We're still supporting the current dynamic_options functionality. This is a first pass and will be cleaned up as we continue to evolve more tools to use this new approach.
Within tool configs, SelectToolParameter types now include a <select_options> tag set. Several tools have been altered to use this new approach. Other tools we enhanced to
use the ColumnListParameter type.
2007-10-19 20:42:11 +00:00
Greg Von Kuster
b3aa4efa6f
Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.
2007-10-03 14:17:41 +00:00
Greg Von Kuster
4c6dab39eb
Enhanced upload utility to dynamically load the File Format select list using values from the registry's datatypes_by_extension dictionary.
2007-09-27 14:12:01 +00:00
Greg Von Kuster
db8eee7889
Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.
2007-09-27 12:24:27 +00:00
Chinmay Rao
18e2c28a45
Added support for gff3 datatype
2007-09-18 15:43:44 +00:00
Greg Von Kuster
02d7abeaa3
Biomart fixes: better handling of max data size, applied data type sniffer.
2007-07-05 20:16:53 +00:00
James Taylor
6aa6c5a2d8
More width hints for data source tools.
2007-07-05 19:20:33 +00:00
James Taylor
4a4c8d25dc
New layouts and style.
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They are somewhat independent (you can use the new layout with the old style
and vice versa) but they belong together.
Tested in Firefox, Safari, IE5.5, IE6, but there are still some features
to be implemented before this is ready for 'main'.
To use, first add "new_style_june_2007=true" to the app:universe section of
universe_wsgi.ini (this gives you the new layout). Second change document_root
to "%(here)s/static/june_2007_style/blue" in the app:static_style section.
Style Features: simplifications, fewer 'hatched' images, space savings in some
places, small changes to the color scheme (same general feel, but the colors
are better matched). Main changes are to history, the new style support nested
datasets much better.
Layout features: no framesets (just iframes, some of which can be replaced with divs and ajax down the road). Frames are resizable and hideable. Tools can provide width hints and history will automatically hide (try UCSC main to see this).
2007-07-05 18:39:36 +00:00
Greg Von Kuster
d312284996
PBS does not like noop command, so eliminating it from Biomart tool.
2007-07-04 18:34:41 +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
Greg Von Kuster
da7aa75ce3
Improved implementation for displaying Galaxy files at UCSC, GBrowse, and other future applications.
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Fixed a bug in the unit test for new gff version 3 format in sniff.py.
Tweaked the biomart tool so that it will not display problm Info: text in history.
This commit includes some stuff for future GBrowse integration, but nothing included should pose any problems with the current environment.
2007-06-28 20:05:11 +00:00
Greg Von Kuster
dbfe147df7
Fixed bug that was causing problems in UCSC Archaea tool.
2007-06-27 16:00:47 +00:00
Greg Von Kuster
a7336bfaa5
Support for Gff version 3 which will be coming from GMOD applications (wormbase, hapmap, etc).
2007-06-26 15:43:57 +00:00
Greg Von Kuster
e7b15fa019
Fixes for BioMart and Subtract Query and another example for Filter.
2007-06-18 20:23:50 +00:00
Jianbin He
30bbb3c1c1
remove tool show_in_ucsc
2007-06-04 14:21:10 +00:00
Daniel Blankenberg
4cbfce361b
Add the ability to define datatypes in the configuration file.
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Datatypes are defined like:
[galaxy:datatypes]
bed = galaxy.datatypes.interval:Bed
png = galaxy.datatypes.images:Image,image/png
where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
2007-06-01 19:25:19 +00:00
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
Greg Von Kuster