An apparatus for generating pressure pulses in a fluid flowing in a downhole tool includes a stator, a rotor, a motor, and an electronics module. The stator and the rotor each have one or more flow passages. The motor oscillates the rotor relative to the stator to align and misalign the flow passage(s) of the stator and the rotor to thereby generate the pressure pulses. The electronics module drives the motor using at least a first signal and a second signal. The motor causes the rotor to have an information-transmitting oscillation in response to the first signal and a cleaning oscillation in response to the second signal.