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 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), 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? Regards, Peter