My question is related to this post 
 in the archive. As recommended, I referred to
 for some guidance on how to achieve multiple output files, specifically one 
set of six files per number of times the <repeat> tag is called. The example 
provided isn't that informative, however, as it doesn't show what the command script is doing so I can make my perl wrapper script do 
the same thing. If I have six files total, do I only specify one in the 
<outputs> tag and then have the remaining 5 named according to the scheme in 
the perl wrapper? Or is it Galaxy that does the naming of the remaining files 
automatically? Is there a perl equivalent to the "$__new_file_path__" variable 
that I can use, or is this the literal resolved file path (e.g. 
"/opt/galaxy/... etc)?

Right now, upon execution of my tool, if a user has two entries (so number of 
times <repeat> has executed is twice), my perl wrapper is called twice (good), 
but on the second call, Galaxy uses the same output filenames as the first run 
such that the first set of output files are all overwritten by the second 
execution (bad). How do I make sure that each <repeat> iteration results in a 
unique set of output files?

Thanks for your help!

Christina Shafer, Ph.D
Regenerative Biology Laboratory
Morgridge Institute for Research
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