Create a Groovy executable JAR with Gradle

What you are looking for is the application plugin which allows you build a standalone JVM application including all dependencies and run scripts.

apply plugin:'application'
mainClassName="test.tree.App"

EDIT:

This should create the uberjar you want:

task uberjar(type: Jar) {
    from files(sourceSets.main.output.classesDir)
    from configurations.runtime.asFileTree.files.collect { zipTree(it) }

    manifest {
        attributes 'Main-Class': 'test.tree.App'
    }
}