You use Tcl commands like this:
set_instance_assignment -name VIRTUAL_PIN ON -to my_pin
Read more in page 15-11 in volume 2 of the Quartus II Handbook:
https://www.altera.com/literature/hb/qts/qts_qii5v2.pdf
Here are a few lines from the chapter:
"Virtual Pins
Usually, when you compile a design in the Quartus II software, all I/O ports are mapped directly to pins on the targeted device. However, you may not want to map all I/O ports to the device pins; use the Virtual Pin assignment then.
A virtual pin is an I/O element that you do not intend to connect to the chip pins. You create a virtual pin by assigning the Virtual Pin logic option to an I/O element. When you compile a design with some I/O elements assigned as virtual pins, those I/O elements become mapped to a logic element and not to a pin during compilation, and are then implemented as a LUT. You might use virtual pin assignments when you compile a partial design, because not all the I/Os from a partial design may drive chip pins at the top level."