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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