On Fri, May 25, 2012 at 4:54 PM, Peter Cock email@example.com:
I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons).
Sorry, that was a typo for EffectiveT3 from http://effectors.org/ (my wrapper is on the Tool Shed).