A typical motorcycle battery is 350 amps.
An amp (short for ampere) is a measure of instantaneous electrical current flow, not electrical capacity. The capacity of a battery is measured in amp-hours, and an FJR battery is rated at 12 amp-Hours. That means (basically) that it will deliver 12 amps of current for one hour and then it is totally dead. Or it could deliver 6 Amps of current for 2 hours. Or 24 amps for 1/2 an hour. You get the picture.
How seriously you discharge the battery depends on the current draw of the pump, the charge level and overall health of the battery, and how quickly you can get the job done. If you discharge your battery too far you had better hope you are at the top of a hill for a bump start.
Or you could just run the bike while you are using the pump.
edit - bradd beat me to the punch.