Chapter 6 Deploying Wireless Networks for FortiOS 5.0 : WiFi-Ethernet Bridge Operation : Bridge SSID to FortiGate wired network : VLAN configuration
  
VLAN configuration
If your environment uses VLAN tagging, you assign the SSID to a specific VLAN in the CLI. For example, to assign the homenet_if interface to VLAN 100, enter:
config wireless-controller vap
edit "homenet_if"
set vlanid 100
end