for running comman line in java use:
Runtime rt = Runtime.getRuntime();
Process pr = rt.exec("MyOtherProg.exe progParameter1 progParameter2");
judging by your comment and question i think you have a class library, and the right way to approach this would be to just create your own C# program that calls the different method on that class library using the given xml as a program args
or other way
Edit
your comment:
unning the exe manually (double click) shows up a wizard with an input
text field and some buttons which does different tasks. the idea is
for our java program to automatically run it and provide the fields
and execute which buttons we would like to trigger to do the function
we want. the java program just automates whatever is done manually
answer:
ok, now we're coking with fire :)
so, at this point i would go to the vendor and ask if i can get a class library instead of the current ui, as you want it running automatically, without Human intervention. while on it i would check if you got other .dll files with the program. if so investigate them using VS.
one last thing, if all is turn bad and you have to do clicks, it's not lost yet, but at this point you have a lot of work, and i can't help you from here, but i'll send you to a link to start what you need and you'll explore from there: