No, it can't be done.
Power is what matters. Using the formula Watts = Volts x Amps, the GPIO can produce at most 3V at 0.04A = 0.12W
Your pump needs 12V at 0.5A = 6W.
Additionally, the GPIO pin voltage will be slightly lower than 3V at full 40mA load and the booster will not be 100% efficient (think of about 75% as a ball park figure) so you actually need even more power than 6W to run the pump.
You can still use the GPIO to control the pump but not to power it directly.
Brian.