I'd stick to Perl. For what you are describing what the tool
needs to do, I figure it would take about the same amount of
work to do it in either Java or Perl. Which means that if your
coders are mainly Perl coders with little Java experience, Perl
would be the way to go.
It isn't wrong to pick a language based on the programming
knowledge that's available. ;-)
I'd be interested to hear what other options you are considering.
C?, C++?, Python?