How to emded JS into XSL script?

Hi,
I have a Java program that runs several XSL scripts against my XML file
to extract the data in HTML format, and then I manually apply the HTML
template (Dreamweaver Template) to each flat HTML page. What I want to
do is to integrate the HTML template into XSL script so that at one pass
I can create the desired output file. 
My question is: Is there any utility out there that would "well-form"
the HTML template so I can integrate it to the XSL script? Or is there a
better way of doing this kind of process?

Thanks..

Cihan 

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