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Run program and close with user interference

I want to run a program that collect data once a day and then close the program.  The problem is I need the user to have access to the program to get it properly configured.  If the program is set to close at completion then the user has no access.  I plan on using the windows scheduler to run the program.  How do I handle this process?  
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Daniel Reynolds
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When you say command switch you mean a command line argument?  Exactly how is this implemented?