Hello Marc,

This issue has been resolve din change set 7491:a7a0a5962648, which will be 
included in the next Galaxy release.  It is also currently available in the 
Galaxy central repository in case you track that repository.  The datatypes 
registry will load any changes you've made to the datatypes_conf.xml file 
installed with the emboss_datatypes tool shed repository (or any other 
repository that includes this file).  SO display_in_upload will now function 
correctly for the installed proprietary datatypes.

Thanks for reporting this issue, and sorry for the inconvenience.

Greg Von Kuster


On Aug 3, 2012, at 4:53 PM, Marc Logghe wrote:

> 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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