In the last section of
"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
"%s_%s_%s_%s_%s_%s" % ( 'primary', output1.id, name, 'visible', file_type,
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
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