Depending on your situation, your various input and output modules might work just as well if you use them as separate filters on the command line. Not knowing how complicated the filtering really is, something like this might (or might not) be a sensible model for usage:

perl -MInput::X -e 'print while($_=Input::X::read)' input.x |  \
  perl -MOutput::Y -pe '$_ = Output::Y::get_output( $_ ) > output.y
[download]

In other words, if you have several different kinds of inputs and outputs, and your modules already address each one separately, then the rest of the "scripting" can be done with the shell command line.

Maybe this would mean doing a little extra work to 'stingify' the intermediate data structure that is shared by the input and output modules. Maybe that would be worthwhile (or not).