gpsbabel -w -r -t -i gpx -f /home/USER/PATH-TO-FILE -o garmin -F /dev/ttyUSB0
You can enter this line also in gebabbel (a GUI for gpsbabel) in "Edit command" to use it from there.
It's dirty (look where your gpsr is connected can be /dev/ttyUSB1 etc. ) works if you get the error: "Claimed interface failed: Device or resource busy"
So for sending the file tour.gpx in the folder Documents in your home directory and your linux-username is mandark e.g. enter gpsbabel -w -r -t -i gpx -f /home/mandark/Documents/tour.gpx -o garmin -F /dev/ttyUSB0