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

#! /usr/bin/perl -w
use strict;
use File::Copy;

my $cmd_string = join (" ",@ARGV);
my $results = `$cmd_string`;
my @files = split("\n",$results);
my $fileNameOut = $ARGV[6];
my ($drive, $outputDir, $file) = File::Spec->splitpath( $fileNameOut );
my $destination = $fileNameOut;

foreach my $thisLine (@files)
{
        if ($thisLine =~ /Created /)
        {
                $thisLine =~ /[\w|\.]+$/;
                $thisLine =$&;
                #print "outfile: $thisLine\n";
                #there is only one file to move, so we can quit after finding it
                move($drive.$outputDir.$thisLine,$fileNameOut);
                exit(1);
        }
        else
        {
                print $thisLine,"\n";
        }
}