On Thu, May 17, 2012 at 12:13 PM, Peter van Heusden <p...@sanbi.ac.za> wrote:
> Hi there
>
> I'm trying to wrap Bioperl's bp_genbank2gff script. This script, by
> default, produces an output file named the same as the basename of the
> input file, with .gff added. So e.g.
>
> bp_genbank2gff data.gbk
>
> produces a file named data.gbk.gff.
>

Is there not an option to specify the output file name? That would
be the easy solution for using this from Galaxy.

> ... Of course the other option
> is to create a tiny wrapper around bp_genbank2gff that takes an output
> filename argument and does the renaming...

Indeed, that is the standard fall back for inflexible tools with a
limited command line API.

Peter
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