So I am assuming that you want to automate something that you run from inside eclipse. if it s a build then I m with the other guys that using a build script and CI is the way to go.
But in case it s not that use case...
Now, if you are using the "Run.." dialogs to do this you can actually get the command line paths, binaries and arguments that eclipse used to execute.
What you do is open up the debug perspective. Then run your script however you normally do.
Your Process should appear in the "Debug View" at this point.
Either while the process is running or after termination, right click on the process and open up the properties. (you may need to click 1 level down in the tree to get this option)
Under process info, inside of that there is a section "Command Line". This is the exact command line that eclipse executed behind the scenes to run.
you should be able to put this into a script (.bat for windows / sh for *nix) and schedule accordingly.
edit: added in assumptions, changed to use process info terms which is what is on the properties screen.