By default, the Team Build server will only compile your assemblies. Creating the necessary manifests, application and setup files necessary to deploy a clickonce application is not executed by default. Enabling this feature is very easy. Edit the TFSBuild.proj file and copy the “SolutionToBuild” line, and put it below, and rename it to “SolutionToPublish”.
1: <SolutionToPublish Include="$(BuildProjectFolderPath)/Source/MySolution.sln">
Team Build will then build the code and place a versioned ClickOnce directory in the drop folder that you can then copy over to your deployment location.