Hi Greg,

> 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.
>

I'am afraid this does not work. At least not in my hands. Like I indicated 
before, it seems like the upload tool does not take the tool shed 
emboss_datatypes into account, with or without the display_in_upload attribute 
set.

It seems to work only if you transfer the entire data type definition line to 
the main galaxy datatypes_conf.xml
That is the workaround I currently use.

Marc


> 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



>> 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

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