tmux_proxy.sh

#!/bin/bash

tmpfile=`mktemp` # name for temp file in /tmp
tmux pipe-pane -t matlab:matlab -o "cat > $tmpfile"
while read line
do
  line=${line//;/\\;} # replace ; with \; to pass send-keys of tmux
  tmux send-keys -l -t matlab:matlab "$line" # send keys literaly
  tmux send-keys -t matlab:matlab Enter
  sleep 0.2s # wait until the commands are put to tmux
done

notFinished="1" # wait until commands are executed
while [ $notFinished -eq 1 ]
do
  A=`awk '/./{line=$0} END{print line}' $tmpfile` # get last line
  if [ A==">> " ]
  then
    notFinished=0
  fi
done

sed -e '/^>>\s*$/d' $tmpfile | # remove >> empty line
  sed -e '/^.*;\s*$/d'  # remove the lines ended with ;

tmux pipe-pane -t matlab:matlab -o #close tmux's pipe
rm $tmpfile