> The header of the Cuffdiff tool page says it is version 0.0.5

This version is the Galaxy tool wrapper version, not the tool version. (Yes, 
this is a usability issue.) You can find the tool version in the dataset's 
information panel by clicking on the 'i' icon.

> Is there a way, or setting, on Cuffdiff 2.0 to revert the parameters to be 
> more similar to Cuffdiff 1.3?

This isn't a parameter issue. The Cuffdiff algorithm has changed substantially, 
and it's not clear to me if/how (or whether it's a good idea at all) to modify 
parameters to obtain 1.3-esque results. 

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