--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flexbar_named_output.pl	Mon Nov 30 07:53:36 2015 -0500
@@ -0,0 +1,50 @@
+#!/usr/bin/env perl
+
+# Flexbar wrapper for Galaxy tool definition, version 2.5
+# Author: Johannes Roehr
+# modified by Daniel Maticzka to include additional user-choosable output prefix
+
+use warnings;
+use strict;
+
+# this parses the last 4 arguments
+# what is id -> xml $output.id
+# what is folder -> xml $__new_file_path__
+# what is format? -> xml $reads.ext
+my ($outFile, $id, $folder, $format, $output_prefix) = @ARGV[($#ARGV - 4) .. $#ARGV];
+
+# this parses all but the last four arguments
+# contains the call to the flexbar actual
+my $call = join " ", @ARGV[0..($#ARGV - 5)];
+
+# this calls flexbar and
+# prefix for output files will be "FlexbarTargetFile"
+system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
+
+# now we parse all output files
+foreach(<FlexbarTargetFile*>){
+
+	# determine filetype
+	my $fileType;
+
+	$fileType = $1         if /\.(\w+)$/;
+	$fileType = $format    if /\.\w*fast\w$/;
+	$fileType = 'fasta'    if /\.fasta$/;
+	$fileType = 'csfasta'  if /\.csfasta$/;
+	$fileType = 'tabular'  if /\.lengthdist$/;
+
+	# this is just the filename from the for loop
+	my $file = $_;
+
+	# replace underscores by minus in $_
+	s/_/-/g;
+
+	# set new name for output files
+	my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
+
+	# rename output file to a pattern recognized by flexbar?
+	rename $file, $name;
+	# best guess: this seems to move the file into a folder
+	# rename behavious is not specified by perl... or implementation differs.
+	rename $name, $folder;
+}