Should you need to the non-oneliner solution, you might want to try the following:

open (INFILE, "<myfile.txt");
open (OUTFILE, "<myfile.txt");
while (my $row = <INFILE>) {
    $row =~ s/~/\r/g;
    print OUTFILE $row;
}
close (INFILE);
close (OUTFILE);
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Michele.