The menu User Tools allows you to make up to 3 new menu commands for calling programs ouside jPreTeX.
By
example if you want to create a menu command calling a program named "Scilab" you click on the user tool menu command ; then a dialog box opens and you type the Name of your tool, here for instance "myScilab", then you fill the field Loading path, for instance "/home/scilab/bin/scilab" under Unix or "C:\scilab\bin\scilab" under Windows. Finally you click on the OK button.
Now if you click again on the menu User Tools you have a new menu command named myScilab and a click on it call this program. The same for 2 other programs.
To remove such a command menu, right click on it and answer "Yes" to the message.
This is saved in your home directory as a file "userTools.cfg" so now on your jPreTeX contains these menu commands.