What exactly do you mean when you say the received 850 “is of different structure?” There are different versions of 850s and each has a standard that must be followed. Each version you will process must be installed into TN. For example, if a partner is sending 4010 850s via the VAN, then you must install the 4010 version of the 850 in TN. Refer to the EDI for TN docs for info.
You will most likely need to create one or more EDI TPAs. In the past, I used an approach where the default TPA was intended for use by all incoming interchanges, since we handled them all the same way. Then we created an EDITPA for each outbound partner. This kept the number of TPAs down.
TN will do the deenveloping for you. Your service that is invoked by the processing rule will receive a single 850 as input for processing. Just map out the data elements from the 850 to whatever structure your flat file needs.
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