Message box arises while simulating the model with hardware connected.

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I need to reset the microcontroller when the code is ready for the flashing.
I get pop up message box to reset the controller after the code being generated while simulating the model.
I have several test cases in signal builder. So, for each case I need to wait for the message box and reset the controller.
I need to automate this process. How can I automate this or how can I detect the message box in between the simulation.

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