One issue when working in that scenario is that you MUST have at least a simple link from input to output to have GENTRAN produce an outbound segment. IOW, you may have to set up an extended rule on the inbound side, predicated on some field that will always have value in the inbound data, to do some populating of temp vars on the inbound side and then link those from the inbound to the outbound.
What is the trans/segment that you are trying to output and what type of data will have to be generated for the segment in question?