Injector injector = new MyDslStandaloneSetup().createInjectorAndDoEMFRegistration();
XtextResourceSet resourceSet = injector.getInstance(XtextResourceSet.class);
resourceSet.addLoadOption(XtextResource.OPTION_RESOLVE_ALL, Boolean.TRUE);
Resource resource = resourceSet.getResource(
    URI.createURI("platform:/resource/org.xtext.example.mydsl/src/example.mydsl"), true);

// Create factory and injector
EMFModelFactory factory = new EMFModelFactory();
EMFInjector injector = new EMFInjector();
// Load the DSL metamodel
EMFReferenceModel metamodel = factory.newReferenceModel();
injector.inject(metamodel, YourDslResource);
// Load the XtextResource as an EMFModel
EMFModel model = factory.newModel(metamodel);
injector.inject(model, resource);
// Launch the transformation as usual
... 

package org.xtext.example;

import java.io.IOException;

import org.eclipse.emf.common.util.URI;
import org.eclipse.emf.ecore.resource.Resource;
import org.eclipse.emf.ecore.xmi.impl.EcoreResourceFactoryImpl;
import org.eclipse.xtext.resource.XtextResourceSet;

public class ModelGenerator {

    /**
     * @param args
     */
    public static void main(String[] args) {
        PropStandaloneSetup.doSetup();
        XtextResourceSet resourceSet = new XtextResourceSet();
        URI uri = URI.createURI("src/test.prop");
        Resource xtextResource = resourceSet.getResource(uri , true);
        Resource xmiResource = new EcoreResourceFactoryImpl().createResource(URI.createURI("src/test.ecore"));
        xmiResource.getContents().add(xtextResource.getContents().get(0));
        try {
            xmiResource.save(null);
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
               
    }

}

outModel.getResource().setURI(URI.createURI("src/ExampleFinal.mycontroller"));