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To write batch files, I configure an Output tool as a csv output, but then update the output path from my workflow with the .bat extension. A Run Command tool can be used to execute the batch file that you have just written. I would also suggest using a Block Until Done tool before your Run Command to make sure everything upstream from that tool is complete before executing the batch file.
If the file you are copying is a format that Alteryx supports, you could open the file, update the location, and re-save it in the same workflow much easier than running batch files.