Scriptella Tutorial provides an example of calling ETL files from Java. You can simply add 3 lines sequentially:
EtlExecutor.newExecutor(new File("etl1.xml")).execute();
EtlExecutor.newExecutor(new File("etl2.xml")).execute();
EtlExecutor.newExecutor(new File("etl3.xml")).execute();
These methods are synchronous, hence the etl files will run one after another.