Something like 

perltidy script.pl && cat script.pl.tdy >script.pl && rm script.pl.tdy

[download]

Note, that it doesn't create backup.

Update: another approach is to dereference symlink: 

perltidy -b `readlink script.pl`

[download]

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

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