I'm not sure about keeping the actual formating (indents, line breaks, comments), but what you're basically looking for is XSLT.

There exists in CPAN a few different XSLT modules (XML::XSLT, XML::LibXSLT, XML::ApplyXSLT), but I've never used any of them.

(I do enough XML work that I know of XSLT, yet never used it directly)