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?