After reading your post four times, I still don't quite get what you're asking for, but I try to be as much of a help as possible. It would be really helpful if you could post a snippet of what you've tried, the "errors" and what you'd like it to do ;)

If I understand correctly, you have a script ready to pump out some data to HTML::Template templates. And, you want to add one variable (named "contig") to some template.

First of all, you need to set this variable within your Perl script:

$template->param(CONTIG => 1);
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After that, you can build the if-statement in the template like this:

<TMPL_IF NAME="CONTIG">
   ... do something, if CONTIG is true ...
<TMPL_ELSE>
   ... do something when CONTIG is false ...
</TMPL_IF>
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jeffa wrote a nice tutorial (HTML::Template Tutorial) which may help you out, but the POD (HTML::Template) is quite readable as well and offers a little more information.

HTH