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I am able to run my own BAT file, but I had to write the code and place the BAT file in the temp folder. This is for an app that I've published to my company's Gallery. The app always creates a BAK file in the destination folder, so I created a temporary BAT file that deletes that BAK file.
As seen here, I have:
A subroutine that generates the code in the BAT file
An Output Data tool that creates the BAT file in the temp folder