The ATL Core API allows to inject/extract models and run transformations programmatically (some concrete examples can be found from there).
Using it, you will be able to do the same that what you are doing with ATL ANT tasks.
Best regards,
------------------------------------------
Hugo Bruneliere - R&D Engineer
AtlanMod research team (Inria, EMN & LINA)
Ecole des Mines de Nantes
Nantes - France
------------------------------------------