Using Treated as the first factor is most likely what you want to do. The example under "What it does > Inputs" of the lower help section for the tool has an example that addresses your use-case.
As with most tools, options are explained on the tool form (abbreviated) and these match up with the underlying wrapped tool's linked manual help (and often publication). Many tools also have a google group/support resource and are frequently discussed by the larger Bioinformatics community at https://www.biostars.org/. Scientific advice would be applicable whether using the tool in Galaxy or not.
Hope that helps! Jen, Galaxy team