Hi Marc,

You'll need to add the display_in_upload attribute to your local version of the 
datatypes_conf.xml file installed with your emboss_datatypes repository from 
the tool shed.

This may result in a merge at some point if the contents of the 
datatypes_conf.xml file changes in the emboss_datatypes repository in the main 
tool shed and you pull the updates to your local repository.

Greg Von Kuster


On Aug 3, 2012, at 10:51 AM, Marc Logghe wrote:

> 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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> hereby notified that any dissemination, distribution or copying of this 
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> in error, please notify us immediately at abl...@ablynx.com. Thank you for 
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> ________________________________________
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