This is a quick reference on how to configure arquillian tests with a tomcat-6 container with gradle.

configurations {
    inContainerTestRuntime { extendsFrom testRuntime }
}

dependences {
    // add any other dependencies you need
    inContainerTestRuntime 'org.apache.tomcat:dbcp:6.0.29',
            'org.jboss.weld.servlet:weld-servlet:1.1.0.Final',
            'org.jboss.arquillian.container:arquillian-tomcat-embedded-6:1.0.0.Alpha4',
            'org.jboss.arquillian:arquillian-spi:1.0.0.Alpha4.SP1',
            'org.jboss.arquillian.protocol:arquillian-protocol-servlet-3:1.0.0.Alpha4',
            'org.jboss.shrinkwrap:shrinkwrap-extension-tomcat-6:1.0.0-alpha-11'
}

sourceSets {
    inContainerTest {
        runtimeClasspath = sourceSets.test.runtimeClasspath + configurations.inContainerTestRuntime + sourceSets.test.resources
    }
}

task inContainerTest(type: Test) {
    classpath = sourceSets.inContainerTest.runtimeClasspath
    include '**/*InContainerTestSuite.*'
}

This has not been fully optimized yet, the runtimeClasspath for inContainerTest sourceSet is probably redundant (I think that sourceSets.test.runtimeClasspath includes resources)