Commit Graph
14 Commits
Author SHA1 Message Date
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 88239abf5c Add more distribution tool citations.
xref #361.
2015-10-05 15:16:50 +01:00
Daniel Blankenberg f92b25d2f5 Enhance tool parameter sanitization. Sanitization rules can now be defined on a per input parameter basis. Resolves ticket #38 and #142.
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
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 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
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
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 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
Guruprasad Anada 550da8f952 Modified the way biomart tool runs: output generation will be completed before exec_afer_process hook is called. 2008-09-30 15:30:57 -04:00
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
James Taylor 6aa6c5a2d8 More width hints for data source tools. 2007-07-05 19:20:33 +00:00
Greg Von Kuster 5b345d0b4c Changed behavior of history import and added BioMart test instance. 2007-05-11 13:06:30 +00:00