Create a user account. Locate the file that you only want the one tool to access and remove all other permissions, then grant the user account you created permissions to the file.
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Next, configure the program to run as the user account you created.
This should allow the program to run as the user account that has rights to the file and, thus, can access the file. The drawback, however, is that if a user logs in as the user account, he will have access to the file with any programs he's running. Similarly, any other programs configured to run as the user account will also have access to the file.
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