I've read about this problem on related posts found here at Superuser; however, my issue is slightly different and potentially difficult to solve: I am working with a phylogenetic program called Paup*, and have written a batch script to automate my analysis.
To automate this process, my batch script creates a temporary file containing a series of 'jobs' for Paup* to execute. Thus, my batch file does not interact with the Paup* application directly (Paup* has its own command line interface).
Halfway through each iteration of my analysis, Paup* requests a user input (Y/N format) for an option that I can NOT pre-specify in my job file. I've looked through the command manual and can not find a way to suppress this dialog prompt either.
Essentially, I need to submit a keystroke directly to Paup*, but only when Paup* explicitly asks me for input. Otherwise the submission will go unresponsive since inputs are not queued. Is there a way I can accomplish this?