Resolve the link before passing it to perltidy. 

for q in * ; do perltidy $(readlink -e "$q") ; done

[download]

You could also modify perltidy to resolve links using Cwd's realpath.

In both cases, the backup will appear next to the linked file.

In reply to Re: Perltidy with symbolic links by ikegami
in thread Perltidy with symbolic links by notwitch

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