How to send commands without typing it on the serial monitor?

Oh, I think I got your question wrong. I think they are then connected by physical means, that inputs/outputs are all connected to FPGA by wires (embeded in the large board).

btw, I really don't think this code would help anything, but still upload.
I'm just using arduino as serial communicator & ADC.


int adc = 0;
int ADC_0,ADC_1;

void setup() {
  Serial.begin(115200);
  pinMode(7,INPUT);
  ADC->ADC_MR |= 0x80; // Mode FREERUN
  ADC->ADC_CR = 2; // Start converter
  ADC->ADC_CHER = 0xFF; // Enabling channels
}

void loop() {
  
  if((PIOC -> PIO_PDSR & 0b00000000100000000000000000000000)>>23 == HIGH){
  ADC_0 = ADC->ADC_CDR[7];// read data on A0
  ADC_1 = ADC->ADC_CDR[6];// read data on A1

  Serial.print("ADC0 Value =");
  Serial.print(ADC_0 / 4 );
  Serial.print(", ADC1 Value =");
  Serial.print(ADC_1 / 4);
  
  Serial.print("\n");
  Serial.print("\n");

  }
}