Pump your no longer flat tire about half way up to its normal pressure and inspect again to make sure the tire is properly seated on both sides all of the way around the rim. If all looks good finish pumping the tire up to your normal riding pressure or to the tires recommended pressure.
Mount your wheel back onto your bike being careful to get the axle properly seated into the dropouts so the wheel runs straight and your brakes are lined up properly. Always make sure your wheels are properly mounted according to the manufacturers instructions.