How can I ask user for input as part of the workflow run?

You can use the Select and Ask local services/processors (Available Services > Local Services > ui in Taverna 2.x, or Available Processors > Local Services > Local Java Widgets > ui in Taverna 1.7.x).

Select lets the user select from a list of options. Ask lets the user type in a value.

In Taverna 1.7.x, you can also use the Interaction Service.