I never realized how immature a lot of Opeth fans are. I mean "so called friends"?! It's not like the dudes slightly ignorant opinion on music makes him an asshole. Jeez.
Anyway, I think your friend was probably comparing damnation to thirteenth step, which is stupid because there's no possible way that album could have influenced damnation. Damnation was recorded in 2002, and thirteenth step didn't come out till 2003. The only other A perfect circle album-mer de noms, sounds nothing like damnation. I can't think of any Tool albums that sound similar enough to it to have been an influence either.
Oh, and just to give my two cents on the whole "who's better" aspect, I think Opeth are a bit more unique as far as composition and arrangement goes. Tool are great and all, but I think a lot of it is more hype then pure musicianship. Not trying to bash on them, but I've never really been able to see why so many people think they're the best band out there. To their credit, it is a mostly rewarding experience, but on the other hand Tool lyrics just plain SUCK compared to most Opeth lyrics.