Run the tstxtract.exe command with the -i switch to run it in-process to create the output.
e.g. tstxtract -i user_email.eml c:\temp_tstxtract\
Note: Where spaces exist in the input file name you will need to surround them with quotes to avoid error
e.g. tstxtract -i "c:\emails from users\user email.eml" c:\temp_tstxtract\