How to automate a Java program in Windows?

How to automate a Java program in Windows?

I have a question that needs an answer in relation to a problem that needs
a solution. However, the answer may be too broad and I completely
understand if the broadness warrants a closure of this question.
I'm using an application that was developed in Java and that connects to
an API. I use this application via command line in Windows 8 to pass 2
core arguments. The first argument is my flat file and the second argument
is my output destination. I can supply any amount of flat file arguments,
but only one output destination.
When I run this application with the arguments listed above, it sends the
flat file and returns another flat file in response. I want to potentially
store this returned flat file in a database of some sort.
Question: My environment is Windows 8 for now and my potential database is
SQL Server 2008. What is the best process to pass multiple flat files to
this Java application automatically that uses a command line via a script
supported by Windows?
java TestClient D:\input_files\test.txt D:\output_files\