On Wed, Feb 29, 2012 at 6:12 PM, Edward Kirton <eskirton@lbl.gov> wrote:
great suggestion; i'll make those changes

Hi Edward,

It has taken me a while but I'm how trying to use HMMER3, and do so
from within Galaxy.

I've realised that the per sequence and per domain tables from hmmscan
and hmmsearch (via the --tblout and --domtblout switches) are NOT tab
separated, but space separated to give an eye pleasing column based

However, your wrapper tells Galaxy they are "tabular". As a result,
Galaxy treats them like tables with one column, which means all the
table operations like filtering on a particular column are not possible.
Has this not affected your users?

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).

Would you agree that a wrapper script to reformat the HMMER3 tables
into tab-separated tables would be the best solution? Would you accept
a code contribution to do this?