How can you tell which are automatic and which are not..

For the perk trees

For a completely accurate answer to that, someone would need to look at the lists of weapons affected by the perks in the game data files.

But for a rough rule of thumb, if it shoots multiple bullets/beams with one press of the trigger it's an automatic; if it only shoots one bullet/beam per press, it's not. I'm sure we'll find some weapons have been improperly classified as time goes on, however - it is a Bethesda game after all.