There are many excellent templating modules around. If you need to expand your script later to do more complicated things you might regret that you didn't use one of those from the beginning

Since you have about 12 replacement patterns it might be worthwhile to combine them into one regex. Using the regex switch e and an array to store the input list you could do something like this:

my @input = split(/,/,$_);
my $file_out= pop @input;
...
foreach ...
...
  $_=~ s/<<<Variable_(\d+)>>>/$input[$1]/ge;
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Untested. Also will give out warnings if there are fewer input parameters on the command line than in the file. A solution would be to change regexp line to

$_=~ s/<<<Variable_(\d+)>>>/if ($1>=@input) {''} else {$input[$1]}/ge;
[download]