Spring Boot does not seem to pick up Atomikos when used for tests

Question

I am working on a prototype for using Spring Boot in our project. We have a JBoss server in production and I was thinking of running integration tests against Undertow embedded server using an embedded transaction manager like Atomikos, because a persistence.xml exists that I have to reuse. My test app context file has the following lines:

@RunWith(SpringJUnit4ClassRunner.class)
@SpringApplicationConfiguration(classes = Application.class)
@WebAppConfiguration
@EnableAutoConfiguration
@IntegrationTest("server.port:0")
@ActiveProfiles("test")
public abstract class TestApplicationContext  {
...
}

I have also added a custom test configuration as:

@Configuration
public class TestConfiguration {
    @Value("${spring.jpa.hibernate.dialect}")
    private String dialectClassName;

    @Value("${spring.jpa.hibernate.transaction.manager_lookup_class}")
    private String transactionManagerClass;

    @Bean
    public EmbeddedServletContainerFactory servletContainer() {
        return new UndertowEmbeddedServletContainerFactory(9000);  // Don't know if this can be avoided using some properties
    }

    @Bean
    @ConfigurationProperties(prefix = DataSourceProperties.PREFIX)
    public DataSource dataSource() throws Exception {
        return DataSourceBuilder.create().build();
    }

    @Bean
    public LocalContainerEntityManagerFactoryBean entityManagerFactory(EntityManagerFactoryBuilder builder,
                                                                       DataSource dataSource) {
        LocalContainerEntityManagerFactoryBean entityManagerFactoryBean =
                builder.dataSource(dataSource).persistenceUnit("main").build();
        Properties additionalProperties = new Properties();
        additionalProperties.put("hibernate.dialect", dialectClassName);
        additionalProperties.put("hibernate.transaction.manager_lookup_class", transactionManagerClass);
        entityManagerFactoryBean.setJpaProperties(additionalProperties);
        return entityManagerFactoryBean;
    }

    @Bean
    public PlatformTransactionManager transactionManager() {
        // this should not be needed if I have included Atomikos but it seems to pick 
        // JPA Transaction manager still and fails with the famous NullPointerException at
        // CMTTransaction class - because it cannot find a JTA environment
        // return new JtaTransactionManager(userTransaction, transactionManager);
    }
}

My gradle include for Atomikos is:

testCompile('org.springframework.boot:spring-boot-starter-jta-atomikos')

I am using Spring Boot 1.2.0-RC2.

CAn someone point out what I am doing wrong or how to solve this?

Thanks,
Paddy