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
Daniel Blankenberg
446f677bdd
MAF Filter tool now accepts comma separated lists of chromosomes.
2007-11-08 21:57:27 +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
382d9d1a51
Rewrite MAF Stitching Tools to store sequence data on disk.
2007-11-07 18:37:13 +00:00
Daniel Blankenberg
8773ecb8d6
Missing metadata for several tools will now result in a user friendly message about setting metadata, instead of a stacktrace.
2007-10-31 15:27:17 +00:00
Daniel Blankenberg
96afd6bf8d
Removing old/unused files for maf tools (mostly config files for user only versions).
2007-10-30 19:47:33 +00:00
Radhesh Kamath
24a37165a3
interval2maf tool now uses dynamic_options.py. \
...
No need for _code file.
2007-10-30 17:21:30 +00:00
Greg Von Kuster
9d363a7efd
Added a test for gene_bed_maf_to_fasta_user option in the GeneBed_Maf_Fasta1 tool.
2007-10-30 15:29:50 +00:00
Greg Von Kuster
518a2d66a8
Bug fix in subtract_query1, made CustomTrack.sniff() more restrictive.
2007-10-30 13:28:24 +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
Guruprasad Anada
5f6fdfdf64
Enhanced error emssage for get_flanks tool.
2007-10-29 15:44:27 +00:00
Greg Von Kuster
b7190a44c0
2007-10-26 19:28:36 +00:00
Greg Von Kuster
5159e418d1
Modified some of the extraction tools (~/extract) to use new dynamic options functionality.
2007-10-26 12:48:47 +00:00
Greg Von Kuster
1175ae1cf5
Modified some of the data type conversion (~/filters) tools to use new dynamic options functionality.
2007-10-26 12:47:06 +00:00
Greg Von Kuster
276c63fe18
Modified some of the maf (~/filters) tools to use new dynamic options functionality.
2007-10-26 12:44:13 +00:00
Greg Von Kuster
49d6c4584b
Enhancements / fixes to new approach to generating dynamic options. Fixes to aggregate scores and wiggle to simple tools. All functional tests should now pass.
2007-10-26 12:38:56 +00:00
Greg Von Kuster
ec1f6a468f
Fixed Bed.sniff() and changed all old bed / interval test data files to work correctly with the new version. Corrected bugs in Gff.set_meta() and Gff3.set_meta(). Commented out test1 in subtract_query.xml until I can determine how to correct twill to properly handle the test with the new approach to using dynamic_options.
2007-10-25 17:18:46 +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.
...
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
fb569d3c43
More ColumnListParameter cleanup. Eliminated dynamic options from some tools by using ColumnListParameter.
2007-10-18 17:29:47 +00:00
Guruprasad Anada
42c130c85b
Changed tool initialization error handling (from stack traceback to simple error message.)
2007-10-17 14:42:35 +00:00
Greg Von Kuster
4f8eb6578b
Various tool fixes, eliminated now unnecessary "refresh_on_change", eliminated old aggregation tool, fixed db conditional in mapping.
2007-10-12 13:11:17 +00:00
Guruprasad Anada
cd1b9436fe
Modified "Gene Bed to Exon/Intron/Codon BED" tool to handle codons falling in the boundary of two consecutive exons.
2007-10-10 15:08:16 +00:00
Greg Von Kuster
0f9cff922c
Miscellaneous tool bug fixes.
2007-10-09 18:51:50 +00:00
James Taylor
13608b5a8b
Cleaning up ColumnListParameter and related things.
...
- Dependencies between parameters and refresh_on_change are now more general.
Any parameter can assert a dependency on any other parameter by name, and
if a parameter has dependencies it will cause a refresh.
- Use "other_values" to get at the value of the associated dataset rather
than trying to look at the tool. This means that column lists now work
inside grouping constructs.
- Eliminated tool.updated_params and use of self.legal_values. These
variables are GLOBAL. Everybody using a tool has a reference to the same
instance of tool. Thus, if two people are using the same tool at once this
can cause serious problems.
2007-10-08 19:33:23 +00:00
Greg Von Kuster
43afaf3969
Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().
2007-10-05 18:02:33 +00:00
Daniel Blankenberg
96a90a5072
Get path for twoBitToFa binary from path of executing script.
...
Should this binary be part of the distribution?
2007-10-05 00:47:35 +00:00
Daniel Blankenberg
207f3ce455
Python is used to run python scripts.
2007-10-04 23:31:38 +00:00
Greg Von Kuster
aa0dcc81d5
More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.
2007-10-04 14:14:15 +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
Daniel Blankenberg
a3b137d94b
Extracting Genomic DNA can now result in an interval file with the
...
sequence appended as a new column.
2007-09-25 16:12:37 +00:00
Daniel Blankenberg
5b85146754
Species are no longer selected by default in MAF tools.
2007-09-21 14:55:06 +00:00
Daniel Blankenberg
1047e7728e
Improve error message on maf tools, telling users where to go to set
...
their genome build.
2007-09-20 20:39:05 +00:00
Greg Von Kuster
20126a37a4
Bug fixes, enhancements (including a new test) for the aggregate_binned_scores_in_intervals tool and added new code file for handling tool exceptions.
2007-09-19 19:45:28 +00:00
Greg Von Kuster
23fd74c2c5
Better error handling for tools that use columnlist tool parameter.
2007-09-19 14:49:02 +00:00
Greg Von Kuster
f27c590190
Enhanced grouping tool to use columnlist tool parameter.
2007-09-18 20:31:09 +00:00
Chinmay Rao
18e2c28a45
Added support for gff3 datatype
2007-09-18 15:43:44 +00:00
Guruprasad Anada
026bc2c6c9
Changed the output type of get_flanks tool to 'interval' so as to ignore the extra BED fields while displaying the data in UCSC. Also skipped lines with negative start/end co-ordinates.
2007-09-18 15:33:01 +00:00
Greg Von Kuster
50968827e9
Enhanced sort tool to use columnlist tool parameter, altered functional test to work with new version. Some other miscellaneous cleanup.
2007-09-17 20:48:59 +00:00
Greg Von Kuster
8b951a529b
Bug fixes, enhancements for cor tool, it now uses the columnlist tool parameter.
2007-09-17 14:21:24 +00:00
Guruprasad Anada
20244dabf6
Modified "UCSC gene BED to Exon/intron BED" tool to include an option for extracting CODONS.
2007-09-12 18:54:10 +00:00
Jianbin He
f0e1e5fa0d
specify the ftype for testing data
2007-09-10 16:16:38 +00:00
Greg Von Kuster
6ebc7a706e
Fixed scatterplot tool to use ColumnList parameter and deleted some unused files.
2007-09-07 13:58:08 +00:00
Greg Von Kuster
543fa44fcf
Bug fix to ColumnListParameter, enhanced Count1 tool to use ColumnListParameter, cleaned up code.
2007-09-06 18:42:59 +00:00
Daniel Blankenberg
6b555a51cb
Allow tests to work with conditional statements.
2007-09-06 17:51:29 +00:00
Greg Von Kuster
c3538a55b7
Enhanced histogram tool to use new columnlist parameter and cleaned up the tool code.
2007-09-04 20:16:33 +00:00
Daniel Blankenberg