At present, Workflow Desinger supports only 4 basic data types. But when a user creates a custom cmdline worker it could send/receive the files with unknown file formats (so, it is probably the new data types). See:
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/55#55
http://ugene.unipro.ru/forum/YaBB.pl?num=1326766085/56#56
So, users could create workers that works only with "known" file formats. If it is an input data, then this problem could be resolved using the "Get file list" + the "String value" format. But it is unresolvable for the output data.
Possible solution: support "String value" data format for output slots of external tool workers.