Atmega32U4+Arduino boorloader+Atmel Studio 6

Hello guys,

i made my own breakout board with the atmega32U4, programmed Arduino bootloader with Usbtiny programmer and was able to upload sketches with Arduino IDE to the board. I am trying to figure out how to upload .hex files through AVRdude diretly and of course, I need to manage the open-clode-open-close of my COM12 that will activate the bootloader virtual comport COM13, which avrdude would need to use. I don't know how this is done in Arduino bootloader, all I see is this line :

Forcing reset using 1200bps open/close on port COM12
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM12, } => {}
PORTS {COM3, COM11, COM12, } / {COM3, COM11, COM13, } => {COM13, }
Found upload port: COM13

Can this be done with AVRdude ? or through some other tool ? How is arduino IDE doing it ?

Thanks for helping