In Taverna 2.x, you can use the Execute Command Line App local service (Available Services > Local Services > io > Execute Command Line App).
In Taverna 1.7.x, the equivalent is to use the Execute cmd-line app processor (Available Processors > Local Services > Local Java Widgets > io > Execute cmd-line app).
However, this is not recommended as it makes your workflow less portable. That is, to run your workflow you have to have Perl (and any libraries that your script requires) installed on the machine you are using, as well as the Perl script that the workflow references.
If your Perl script is fairly simple you may find a Local Java Service/Widget to do the same thing. If your Perl script is large/complex you may want to convert it into a Web service.
