the GUI is arguably the "least interesting" way of using WFA
SOAP & REST web services interfaces are provided so you can make calls from programs, including routines running on remote systems (links are to reference guides). these are the API.
you might be able to use the perl REST::Client module or similar for easier access.
note that the bulk of the workflow logic usually happens inside WFA
you'll also need to allow for non-blocking execution in your calling code, as WFA works on a kind of batch submission basis: you submit a request to WFA, then check back on the system to check job status at a later stage (which may only be a couple of seconds, but you need to have the right kind of logic in there to poll, rather than expect an execution result directly form the call).