root/galaxy-central/tools/emboss_5/emboss_banana.pl

#! /usr/bin/perl -w
use strict;

my $cmd_string = join (" ",@ARGV);
#my $cmd_string = "/home/djb396/temp/emboss/bin/banana -sequence /home/djb396/universe-prototype/test.fasta -outfile result.txt -graph png -goutfile results -auto";
my $results = `$cmd_string`;
my @files = split("\n",$results);
foreach my $thisLine (@files)
{
        if ($thisLine =~ /Created /i)
        {
                $thisLine =~ /[\w|\.]+$/;
                $thisLine =$&;
                print "outfile: $thisLine\n";
        }
}