assuming you're using an approved emulator, yes. heck you can even use a guitar hero guitar or even a set of drums. you can't use buttons that are Turbo A nor Turbo B though

A Guitar Hero guitar? Who would be stupid enough to run with a guitar? Kappa

Jokes aside, you can run with literally anything you want as long as you don't left+right nor use a turbo

what if i do a run with a controller with the tas programed into it?

Yes.