Hi Björn,
I think the issue is that the genbank datatype is coming in via the tool shed 
and is not taken into account by the upload tool. The genbank datatype is 
defined in 
shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml

I have added the display_in_upload attribute in the latter file for the genbank 
datatype, restarted Galaxy but the type did not appear in the selection.
Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or 
is it better to explicitly add the emboss' datatypes_conf.xml to the 
universe_wsgi.ini (but this will break the tool shed update system, right) ?

Thanks,
Marc

-----Original Message-----
From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] 
Sent: Friday, August 03, 2012 4:14 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ?

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="[ &quot;%s%s%s&quot; % ( 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.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/
________________________________________
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WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, 
CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. 
If the reader of this E-mail message is not the intended recipient, you are 
hereby notified that any dissemination, distribution or copying of this 
communication is strictly prohibited. If you have received this communication 
in error, please notify us immediately at abl...@ablynx.com. Thank you for your 
co-operation. 
"NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. 
________________________________________

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