--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flexbar.pl	Mon Mar 18 18:18:28 2013 +0100
@@ -0,0 +1,34 @@
+#!/usr/bin/env perl
+
+# Flexbar wrapper for Galaxy tool definition, version 2.33
+# Author: Johannes Roehr
+
+use warnings;
+use strict;
+
+my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
+
+my $call = join " ", @ARGV[0..($#ARGV - 4)];
+
+system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
+
+
+foreach(<FlexbarTargetFile*>){
+	
+	my $fileType;
+	
+	$fileType = $1         if /\.(\w+)$/;
+	$fileType = $format    if /\.\w*fast\w$/;
+	$fileType = 'fasta'    if /\.fasta$/;
+	$fileType = 'tabular'  if $fileType eq 'lengthdist';
+	
+	my $file = $_;
+	
+	s/_//g;
+	
+	my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
+	
+	rename $file, $name;
+	rename $name, $folder;
+}
+