Wolfgang Maier
76968a68c7
Adjust UCSC Table browser tools to code changes
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Since the code now drops undeclared incoming parameters it enforces
cleaner wrapper style.
2024-02-22 17:29:33 +01:00
Wolfgang Maier
bd0f257452
Switch data_source.py to modern tool-provided metadata
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Allows moving all data source tools using the script to profile 20.09.
For more recent profiles data_source.py would have to work outside of
Galaxy's Python environment.
2024-02-08 16:43:39 +01:00
Helena Rasche
646b133bb3
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
Nicola Soranzo
ef4f5ccda4
Remove deprecated `interpreter attribute from tools <command>`
2020-03-05 12:53:09 +01:00
John Chilton
a6f9e62c1a
Add citations to ucsc browser tools.
2015-10-05 15:55:21 +01:00
Nicola Soranzo
22d4a1d8c3
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
Daniel Blankenberg
694300ce97
Some reworking of data_source tools and the standard data_source.py script. Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tools' XML configuration files. Auto-detect is now available by providing data_type=auto parameters.
2011-04-21 13:12:10 -04:00
Daniel Blankenberg
3b70b41f7d
Update UCSC table browser datasource tools to treat data marked as 'gff' as 'gtf'.
2010-06-28 11:50:25 -04:00
Daniel Blankenberg
f92b25d2f5
Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142 .
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Sanitization now occurs as part of the InputValueWrapper logic. Previously sanitization occurred as soon as parameter values were provided by the user via form submits, causing the sanitized values to be stored in the database. Now the original user specified values are stored in the database and sanitation happens when str is called on the InputValueWrapper, i.e. during command-line generation and when generating configfiles.
Abstract out param name and value translations that are performed on data source tools. This changes some of the names of the tags used for these purposes (e.g. data_type_translation becomes value_translation) to reflect this generalization. The ToolConfigSyntax wiki page has been updated with these changes.
Future Enhancement:
Allow methods with arguments and keywords to be specified for sanitation and translation purposes.
2009-12-07 10:19:41 -05:00
Daniel Blankenberg
b2e2b801ea
Enhance data_source.py to take advantage of the content length when known. If content length provided by external application is
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greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user.
Tools using this script have been updated to provide the max file size on the command line.
Resolves ticket #93 .
2009-08-03 12:02:54 -04:00
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
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
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
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
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
04e0834500
Revert 2715.
2008-06-04 13:02:15 +00:00
Greg Von Kuster
dedc7278a1
Requires config change, temporary files are now created in a configurable location - affects many tools.
2008-06-03 20:29:54 +00:00
Greg Von Kuster
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +00:00
James Taylor
6aa6c5a2d8
More width hints for data source tools.
2007-07-05 19:20:33 +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
Wolfgang Maier