Hi Marc, please have a look at the datatypes_conf.xml file in your galaxy directory. There should be something like that: <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> Try to add 'display_in_upload="true"' to the genbank datatype. The 'good' solution would be to define a datatype genbank, with a sniff function, so that galaxy can guess the filetype when you are uploading it. Please find attached my first attempt for that. Im working on some datatypes and converteres, but its not ready yet :( Cheers, Bjoern
Hi again,
Emboss_datatypes is installad via tool shed. The ‘View datatypes registry’ in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank.
However, the ‘Upload File’ tool does not show genbank in the ‘File Format’ dropdown. How can one configure the upload1 tool so that all registered formats are listed ?
I don’t understand the from_parameter hocus-pocus in this line (upload.xml):
<options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">
The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ?
Regards,
Marc
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-- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/