In FortiOS version 5.2 Traffic Shaping was configured over firewall policy. By default if traffic shaping wanted to be applied, It was just a matter of create a shaper and point it out on policy.
Now on 5.4 - 5.6 FortiOS versions there is no such option, It has to be configured using CLI every time you want to configure inside the policy.
All FortiGate Version 5.4 / 5.6
1. Go to Policy&Objects > IPv4 Policy, click right over policy which Traffic Shaping will be configured and click “Edit in CLI”
2. Configure the following commands inside the policy:
set traffic-shaper <shaper name>
set reverse-traffic-shaper <shaper name>
end
3. Once configured you will see Traffic shaping configuration in policy by WEB GUI
This steps has to be done on every policy you want to apply Traffic Shaping by policy.