Greg Von Kuster
0160211343
Fix for 1 line interval files that do not include a commented header. Added default values for chrom, start, end for interval format and enhanced set_meta() so that auto-detect button on edit form will work for interval files.
2007-12-04 16:32:14 +00:00
Greg Von Kuster
ab1d867915
More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores.
2007-11-30 20:08:21 +00:00
Greg Von Kuster
396ca8c43e
Uncommented functional tests in some regVariation tools in preparation for moving them to main.
2007-11-30 13:43:59 +00:00
Greg Von Kuster
87c0138d6d
Fixed bug I introduced in quality_filter.xml
2007-11-29 21:25:11 +00:00
Greg Von Kuster
6c4df387b7
Fixed bug when setting peek on a binary dataset. Also fixed up code in 2 functions in root.py.
2007-11-29 21:20:29 +00:00
Daniel Blankenberg
9efcb80fe3
More MAF tools now have better behavior when no species are selected.
2007-11-29 18:13:48 +00:00
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
James Taylor
2a6cb86131
Consolidating workflow templates / controllers
2007-11-28 20:28:46 +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
Daniel Blankenberg
83d2926577
Enhance interval_maf stitching tool to work when no species are selected ==> defaults to providing all species available.
2007-11-28 18:12:03 +00:00
Daniel Blankenberg
b5de2e878e
Enhance validation of dynamic options when no data/info is available.
2007-11-28 17:46:04 +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
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
Guruprasad Anada
49bc4a4da4
Added Regional variation section to tool_conf.xml.sample.
2007-11-20 19:56:01 +00:00
Guruprasad Anada
b52524892e
Regional variation tools: Tool xmls, code files and test-data added for 4 regional variation tools.
2007-11-19 21:55:45 +00:00
Greg Von Kuster
71d16671bc
First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons:
...
axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
2007-11-16 20:08:31 +00:00
Greg Von Kuster
e97522b3a5
Enhanced select list displayed as radio buttons to handle refresh_on_change if we need it in the future.
2007-11-16 20:04:06 +00:00
Daniel Blankenberg
0e9c5bdbd9
Minor update to interval2maf.py display of error messages.
2007-11-16 17:39:49 +00:00
Daniel Blankenberg
538db8bd09
Update test data output for HyPhy NJ tree wrapper.
2007-11-15 17:19:29 +00:00
Daniel Blankenberg
4db24ed949
Minor change to display of diff.
2007-11-15 17:03:00 +00:00
Daniel Blankenberg
48d718bca6
Fix comparison of file contents for test framework. It was previously using zip(), so tests would wrongly pass when one file was smaller than the other (but contained the same data up to it's end).
2007-11-14 22:00:29 +00:00
Daniel Blankenberg
41a885a875
Add validation of metadata before tool run.
2007-11-14 20:50:33 +00:00
Daniel Blankenberg
52fbb2c93b
Missed an import in interval2maf.py. Something real stupid, but it
...
should have been picked up by the tests.
2007-11-14 18:44:41 +00:00
Greg Von Kuster
6e8ff8c545
Anything printed to stderr will once again result in a job error.
2007-11-14 14:12:42 +00:00
Daniel Blankenberg
fdf0dfd3f8
MAF Stats tool should now be more efficient.
2007-11-13 21:00:05 +00:00
Daniel Blankenberg
451ed28c9e
Fix Typo
2007-11-13 18:20:13 +00:00
Daniel Blankenberg
3c545c03ad
Mostly cleaning up MAF tool code. maf_to_fasta_concat.py no longer stores sequences in memory.
2007-11-13 18:17:54 +00:00
Greg Von Kuster
96e3ac8d1b
Fix for new auto-detect form. Also added a new functional test for the auto-detect form.
2007-11-13 14:02:49 +00:00
Greg Von Kuster
f638adb5d3
Added an "Auto-dectect" button to the Edit (metadata) Attributes form.
...
Cleaned up some bugs in Bed and Interval set_meta associated functions.
set_meta() will no longer be called prior to the edit form being displayed since doing this displayed attribute values that were not from the database (misleading the user).
2007-11-12 22:20:06 +00:00
Daniel Blankenberg
6eaa6d511c
Update interval2maf tools to use one script file.
2007-11-12 21:06:24 +00:00
Daniel Blankenberg
a67ae1e50b
In MAF stitching tools, only build the index for the primary species.
2007-11-12 17:44:29 +00:00
Greg Von Kuster
35e95694bc
Fix for sorter tool to allow for "tabular" dataset consisting of 1 column.
2007-11-10 19:50:09 +00:00
James Taylor
2a39285bb3
Fix for building custom tracks from interval files.
2007-11-10 01:32:19 +00:00
Nate Coraor
2d1a7f08f4
a tab accidentally snuck in.
2007-11-09 18:13:08 +00:00
Nate Coraor
3ab97ed098
Added the ability to "brand" Galaxy in the masthead from the ini file.
2007-11-09 16:52:02 +00:00
Daniel Blankenberg
b4a9884081
'Fake' datasets are now built using 'data' as the format type.
2007-11-09 16:37:45 +00:00
James Taylor
bb7c30af07
Updating packed version of panels script.
2007-11-08 23:37:23 +00:00
Daniel Blankenberg
446f677bdd
MAF Filter tool now accepts comma separated lists of chromosomes.
2007-11-08 21:57:27 +00:00
Daniel Blankenberg
29c9521010
Fixes and enhancements for displaying interval/bed files at UCSC.
2007-11-08 20:14:20 +00:00
James Taylor
69ddb7d83f
Remove PassiveDefaults and calculate dates in Python using utcnow. This should
...
be compatible with ALL databases (tested with sqlite and postgres, probably
also eliminates the need for the mysql workarounds we have in mapping.init)
2007-11-08 19:56:10 +00:00
Daniel Blankenberg
0095b818f1
When detecting metadata on a BED type, the whole file no longer needs to be processed to determine
...
existance of strand column. Also added nameCol optional metadata parameter for interval datatypes.
2007-11-08 18:16:32 +00:00
Daniel Blankenberg
d6a6e5c89b
Consolidating MAF stitching tools. No more multiple pages for these tools.
2007-11-08 17:00:18 +00:00
Daniel Blankenberg
2263946fe7
Update test data for MAF stitching tools.
2007-11-07 18:37:25 +00:00
Daniel Blankenberg
382d9d1a51
Rewrite MAF Stitching Tools to store sequence data on disk.
2007-11-07 18:37:13 +00:00
Greg Von Kuster
155e87f9ae
Fix for maf tools that include multiple nested dependents that are affected when one of the form fields is changed.
2007-11-07 14:27:59 +00:00
Greg Von Kuster
094ba6e037
Another commented set_meta(). This should be all for now.
2007-11-02 13:17:18 +00:00
Greg Von Kuster
ffb3be8c38
Comment out set_meta() - tools should now go faster.
2007-11-02 13:05:04 +00:00
Anton Nekrutenko
0c06d9f7e1
Fixing base.css
2007-10-31 20:56:39 +00:00
Anton Nekrutenko
eb69b25b7a
Style template and blue fixes
2007-10-31 20:41:57 +00:00
Jianbin He
cd58c91104
add test section option
2007-10-31 19:12:00 +00:00
Greg Von Kuster