As an additional feature TraceWrangler can apply filters while merging files. The result is that only frames matching at least one filter will end up in the merged output file.
The filter options are limited to simple address and port filters, with some additional TCP flags also being available. This feature is not a replacement for the powerful display filter engine of Wireshark/tshark, it is just a nice thing to have.
After adding a filter you'll see it listed in the filter list in Wireshark display filter syntax. This is only to allow seasoned Wireshark/tshark users to read it in a familiar way. You can't specify filters in that syntax manually.