sorry for the late reply, i've been away for almost a month.  thanks for
your work on this, i'll update the tools and upload to toolshed asap.

On Tue, May 29, 2012 at 3:35 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Fri, May 25, 2012 at 4:54 PM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
> > 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
> > layout.
> >
> > 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), EffectiveT3 (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?
> >
> > Regards,
> >
> > Peter
>
> Hi Edward,
>
> I've written a simple HMMER3 table to tabular script in Python,
> https://github.com/peterjc/picobio/blob/master/hmmer/hmmer_table2tabular.py
>
> Would you prefer to:
>
> (a) amend the XML to call HMMER, and then call the conversion script
>    twice.
>
> (b) turn this into a single wrapper script which calls HMMER3 and
>    then converts the two tables (using a multiple command line call
>    with shell semi-colon separators).
>
> (c) do something else?
>
> I favour the wrapper script option as more flexible in the long run (e.g.
> for
> error handling and splitting jobs over multiple machines), and the multiple
> command approach may lead to overly long command line strings.
>
> Peter
>
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