use strict;
my $str = '[[<name> (<identifier>)|<name>]]
>>>
{{<template>|<link>|<identifier>}}
====[[<link #1>]] [[<link #2 name> (<link #2 identifier>)|<link #2 name>]]====
[[<link #3 name> (<link #3 identifier>)|<link #3 name>]]';
my $regex = qr/\[\[((?:(?!\[\[)[^()])*)\s+\(((?:(?!\[\[)[^()])*)\)\|(.*?)]]/mp;
my $subst = '{{<template>|$1|$2}}';
my $result = $str =~ s/$regex/$subst/rg;
print "The result of the substitution is' $result\n";
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Perl, please visit: http://perldoc.perl.org/perlre.html