How do I run a Perl script / command line from Taverna?

You can use the Execute cmd-line app processor (Local Services > Local Java Widgets > io > Execute cmd-line app). However, this is not recommended as it makes your workflow less portable, i.e. to run your workflow you have to have perl (and any libraries that your script requires) installed on the machine you're using, as well as the perl script that the workflow references.

If your perl script is fairly simple you may find a Local Java Widget to do the same thing. If your perl script is large/complex you may want to convert it into a web service. See What is the best way to make a web service that can be used by Taverna?