ModelFactory mf = AtlParser.getDefault().getModelFactory();
IReferenceModel atlMM = AtlParser.getDefault().getAtlMetamodel();
IModel atlM = mf.newModel(atlMM);

EObject module = (EObject) atlM.newElement(atlMM.getMetaElementByName("Module"));
module.eSet(module.eClass().getEStructuralFeature("name"), "testmodule");
EObject rule = (EObject) atlM.newElement(atlMM.getMetaElementByName("MatchedRule"));
rule.eSet(rule.eClass().getEStructuralFeature("name"), "Test");
EList<EObject> moduleElements = (EList<EObject>) module.eGet(module.eClass().getEStructuralFeature("elements"));
moduleElements.add(rule);

FileOutputStream fos = new FileOutputStream("testmodule.atl");
try {
	AtlParser.getDefault().extract(atlM, fos, Collections.emptyMap());
} finally {
	if (fos != null) {
		fos.close();
	}
}

module testmodule;
create from;

rule Test {
 
}

rule rule1{
	from
		sys:Source!System 
}

-- @atlcompiler emftvm
-- @nsURI ECORE=http://www.eclipse.org/emf/2002/Ecore
-- Alphabetically sorts the contents of an Ecore model by name.
module SortEcore;

create OUT : ECORE refining IN : ECORE;

rule EPackage {
	from
		s : ECORE!EPackage
	to
		t : ECORE!EPackage (
			eClassifiers <- s.eClassifiers->sortedBy(e | e.name),
			eSubpackages <- s.eSubpackages->sortedBy(p | p.name)
		)
}