Connect windows standalone aplication to command line

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I created a matlab function which needs two variables a load directory and a save directory. With this function i created a windows standalone application with the MATLAB compiler.

I want to run my application in an excisting program in which i will select the data to load. I know the command line of this program is as follows:

program.bat -r /returndir /seriesdir -r0

I assume the returndirectory is my save directory and the seriesdirectory my load directory. My question is how do i start my matlab function and connect it to the command line above?

For example should i start my function like:

Fucntion [output] = MyProgram (returndir, seriesdir)

In othter words how do i connect the directories in my command line to the variables in my function? And is it possible to test this from the cmd prompt?