Set Application Pool for package using MSDeploy

I am deploying a website using MSDeploy so using something like the below code.

"%ProgramFiles%\IIS\Microsoft Web Deploy\msdeploy.exe" 
     -verb:sync
     -source:package=WebAppServer.zip 
     -dest:Auto 
     -setParamFile="was_params.xml" 
     -verbose 
          >  webappserversync.log

Is there anyway to set the application pool ? I want to do this from the command line and not set it in a manifest or anything like that.

Shouldn't matter but this is in IIS7.