Yes, running out of gas while attempting to set the emission monitors (complete a drive cycle) will more than likely require that you complete another drive cycle.
Normally "idling" your car would mean having the vehicle in PARK and allowing the engine to simple run; no movement of the gas pedal. "Idling on Drive" means having the vehicle in DRIVE and your foot on the brake pedal with no engine acceleration or vehicle movement.
Take extreme caution when performing drive cycles on public roadways. Perform any drive cycle procedure at your own risk. If you feel you may be unable to perform a drive cycle safely please visit your local auto service center.