On Fri, May 25, 2012 at 4:54 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

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).