How to check clocks using SignalTap II Logic Analyzer?

jtag_debug_sample_clock does just that, it reads the clock signal at the time you ask for it, so sometimes you'll get a 0 and sometimes you'll get a 1.

jtag_debug_sense_clock returns 1 if the clock toggled since the last time you called jtag_debug_sense_clock and 0 otherwise. You may get a 0 after the first call (I never did, but you never know) but after that you should only get 1's. If you get 0's after then you probably have a problem.

In SignalTap if the clock you selected a a sampling clock isn't toggling, SignalTap will tell you so. (I don't remember the exact message, but it's different than 'waiting for trigger')