the user_project_wrapper_empty.mag already has the analog_io pin, so you just need to rout your analog desing to those pins.
the caravel.mag file has the integration of the chip_io.mag and the user_project_wrapper.mag. Here you can see that the analog_io pin form the user_project_wrapper is conected to the PAD_A_ESD_0_h. If you need to connect you analog signal to the PAD_A_NO_ESD, you need to re-route manually this connection.