Hi,
In the last section of https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput, "Number of output datasets cannot be determined until tool run", it should be updated that the new additional datasets file format actually has a sixth part at the end where you can set the database attribute of the output dataset:
"%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type, database )
I accidentally discovered this even though I didn't want to set the database attribute because I have some custom datatypes defined and my datatype extension names have underscores in them :) which causes Galaxy to think that the part of my extension names string after the underscore is actually the database name i want to set.
I would recommend not to put underscores in your custom datatype extension names :)
-Leandro
galaxy-dev@lists.galaxyproject.org