Token filtering with eclipse-wtp

We have enabled filtering of tokens on process resources, and for webapp on war task. The problem is that we want to run application from Eclipse with wtp plugin, and when we try to do this the tokens are not substituted. My question is if setting the sources to the build result and setting dependency of wtp tasks on war task would be a good idea, or there is some simpler yet better way to tackle this problem?

We are using: Gradle: 1.12 STS: 3.6.1 (based on Eclipse 4.4)