17 May
2012
17 May
'12
12:58 p.m.
On Thu, May 17, 2012 at 12:13 PM, Peter van Heusden <pvh@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