You can apply pin assignments with Tcl scripts, by either entering individual Tcl commands in the Tcl Console, or creating a .tcl script and the typing the following in the command line:
Applying Tcl Script Assignments
quartus_sh -t <my_tcl_script>.tcl
Scripted Pin Assignment
The following example uses set_location_assignment and set_instance_assignment Tcl commands to assign a pin to a specific location, I/O standard, and drive strength.
set_location_assignment PIN_M20 -to address[10] set_instance_assignment -name IO_STANDARD "2.5 V" -to address[10] set_instance_assignment -name CURRENT_STRENGTH_NEW "MAXIMUM CURRENT" -to address[10]