You can try Win32::GuiTest http://search.cpan.org/~karasik/Win32-GuiTest-1.60/lib/Win32/GuiTest.pm and using FindWindowLike , SendKeys APIs, you can send key strokes to Any window (including cmd prompt)
I have done a script some time back to do the similar job.
- start the app / script which needs an input in background and redirect the output to file, (Ex:start perl.exe abc.pl > out.txt 2>&1 )
- Monitor out.txt in your automate script and look for patterns to enter your input
- use Win32::GuiTest and send keystroke to the app/script which was started in background.