Anton Nekrutenko
076398c821
Changed grouping output to tabular
2009-01-22 12:46:37 -05:00
Greg Von Kuster
705994a0fc
Fixes for formatting end of line chars in html when displaying dataset.info. Also change the biomart tool version.
2009-01-22 08:50:52 -05:00
Greg Von Kuster
7e21fb74a3
Fixes for Biomart and UCSC to better ensure the data type is correctly set. A data type of "tabular" is now the default, and data will be sniffed if this is the data type.
2009-01-21 17:03:39 -05:00
Wen-Yu Chung
498fbac868
remove the usage of hast tables in the fasta-tools
2009-01-19 15:47:02 -05:00
Guruprasad Anada
50b46e60e3
Removed an option from grouping tool, which is now part of the LCA tool under Taxonomy.
2009-01-16 13:30:01 -05:00
Guruprasad Anada
ee8779987e
More changes to mutability tool.
2009-01-15 13:10:04 -05:00
Greg Von Kuster
b7aaa17bc3
Change History.copy() back to use datasets rather than active_datasets. Add checks in set_peek() to properly set peek on purged datasets. Fixes sharing a history that contains purged datasets.
2009-01-15 10:49:01 -05:00
Guruprasad Anada
d46171ea21
Fixed a bug in microsatellite mutability tool.
2009-01-15 10:42:22 -05:00
Guruprasad Anada
e25946e9b9
Tool to find the least common ancestor added under Taxonomy section.
2009-01-13 12:18:08 -05:00
Greg Von Kuster
051a78bc39
Add new tool config for flymine production server.
2009-01-13 10:55:08 -05:00
Greg Von Kuster
86c7a80c31
Add support for NCBI Blast XML data format.
2009-01-07 12:20:35 -05:00
Guruprasad Anada
cc80d63745
Added a new option to the grouping tool to facilitate picking of random entries from columns not chosen for either grouping or aggregate operations.
2009-01-06 11:11:24 -05:00
Nate Coraor
d337613eeb
megablast fix from Anton
2009-01-05 15:26:17 -05:00
Guruprasad Anada
8c7c765480
Modified sort options in grouping tool to work correctly on older and newer versions of unix sort. Also included functional tests.
2008-12-22 12:15:02 -05:00
Wen-Yu Chung
b31191d4bd
fix for short read score distribution tool. restore test data.
2008-12-19 14:25:43 -05:00
Wen-Yu Chung
170f9d2d77
fixed for short read build distribution tool. remove unused arrays. also update test data output.
2008-12-19 12:25:52 -05:00
Greg Von Kuster
dfd5e9827f
Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server.
2008-12-15 10:37:39 -05:00
Greg Von Kuster
7a5203fd65
Attempting to merge conflicts.
2008-12-15 08:58:33 -05:00
Greg Von Kuster
b432fd166d
merging heads
2008-12-15 08:55:16 -05:00
Greg Von Kuster
2647f72e4a
Add ability for data_source tools to append parameters passed in the initial response to the value of URL prior to Galaxy's post to the URL. This is a cleaner method for Biomart and also gets GBrowse to wrok.
2008-12-13 23:35:29 -05:00
Guruprasad Anada
9a0953f1f1
Added more test-cases to GOPS JOIN to include cases with different cut-offs for overlap.
2008-12-12 12:12:59 -05:00
Greg Von Kuster
f83ff13b78
Increase the version in the grouping tool due to previously changed output, change the output and increase the version of the gsummary tool.
2008-12-05 09:01:22 -05:00
Daniel Blankenberg
18f4037ba2
Update GMAJ help.
2008-12-04 15:09:57 -05:00
Guruprasad Anada
b88df9bdc3
Bug fixes for compare, Group and filter tools.
2008-12-02 11:41:25 -05:00
Greg Von Kuster
ffa719a9ab
Call set_size() before set_peek() on datasets, changes to set_peek() to not read entire files for some datatypes.
2008-12-02 10:50:54 -05:00
Daniel Blankenberg
7e0479473c
Update GMAJ to latest beta.
2008-11-24 11:19:48 -05:00
Wen-Yu Chung
2ee04d24af
(no commit message)
2008-11-18 11:23:09 -05:00
Wen-Yu Chung
87a68ea595
update poisson test tool for R warnings.
2008-11-14 13:21:02 -05:00
Greg Von Kuster
32b4b77f74
Missed translating the primaryTable data type from UCSC in my last commit.
2008-11-13 15:17:42 -05:00
Greg Von Kuster
c454370ff7
Add a new <data_type_translation> tag set to data_source tools that enable the translation of an unsupported data type to a supported one in Galaxy ( currently only used in UCSC ). Also some tweaks to the jobs reports.
2008-11-13 14:56:33 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Daniel Blankenberg
ad21aee2a0
Small typo in one of the encode import tools.
2008-10-31 14:52:41 -04:00
Daniel Blankenberg
35168f40a5
Fixes for dealing with UnvalidatedValues (i.e. when running workflows) and also when passing None trans to dynamic options.
2008-10-31 11:00:50 -04:00
Greg Von Kuster
5be8fefaf5
Migrate central repo to alchemy 4.
2008-10-30 16:17:46 -04:00
Guruprasad Anada
e35fa87fbd
Added new functional tests to all gops tools using BitsetSafeReaderWrapper. These tests check cases where datasets have the chr,start and end values in non-standard columns.
2008-10-30 16:03:11 -04:00
Daniel Blankenberg
aeaf3c8978
Annotation profiler: Better handling of the case where regions extend beyond known chromosome boundaries.
2008-10-30 14:46:57 -04:00
Greg Von Kuster
7b49309886
Add new EpiGRAPH tools that point to EpiGRAPH production server.
2008-10-28 11:27:42 -04:00
Greg Von Kuster
b74f176613
Add a new URL_method attribute to data_source tool types whose value is either "get" or "post" ( some require a get request while others require a post request ). This fixes the Biomart problem ( along with a new, well documented hack that can be eliminated when Biomart encodes the value of URL in the initial response - they'll tell us when they've fixed this ). Also added some requested info to the "send to EpiGRAPH" tool.
2008-10-27 16:03:43 -04:00
Daniel Blankenberg
b9e242e4eb
Add a new metadata type of Metadata Files.
...
These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
2008-10-22 13:49:22 -04:00
Guruprasad Anada
d6d59f7431
Added Validator to a bunch of tools..
2008-10-17 13:02:26 -04:00
Greg Von Kuster
288912ee87
Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.
2008-10-17 10:46:29 -04:00
Wen-Yu Chung
b3bcbdcf15
update xml files for short reads mapping tools.
2008-10-15 15:51:13 -04:00
Wen-Yu Chung
0021c40c85
add shrimp_color_space mapping tool with functional test data.
...
add a new datatype called csfasta.
2008-10-13 15:06:42 -04:00
Daniel Blankenberg
09ce7a9b17
Maf stats will now use bitset instead of numpy.zerros.
2008-10-09 11:23:33 -04:00
Greg Von Kuster
b3b6c54247
Use only 1 underlying executable ( data_source.py ) for data source tools. A new tag set is added to the data source tool configs to handle tranlsation of request param names sent by remote apps ( something like <param_trans galaxy_name="dbkey" remote_name="GENOME" missing="?" /> ).
2008-10-07 15:21:46 -04:00
Greg Von Kuster
c05f66d5ee
Treat EpiGRAPH as a data source much like ucsc table browser.
2008-10-06 13:34:51 -04:00
Guruprasad Anada
e78f34fb49
Modified help message for indel rate tool.
2008-10-06 09:33:52 -04:00
Greg Von Kuster
53a4390863
Fix for histogram tool when input dataset is empty.
2008-10-01 10:17:58 -04:00
Wen-Yu Chung
d7b7c0795f
add error msg for shrimp_wrapper when memory error and zero hits.
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convert last column of megablast output to float.
2008-09-30 16:40:42 -04:00
Daniel Blankenberg
61ca17eade
Add a change_format tag to output datasets in tools. This allows for dynamic switching of output datatype based upon input values.
...
Several tools have been updated to take advantage of this, eliminating their need for code_files.
2008-09-30 16:17:12 -04:00
Anton Nekrutenko