diff flexbar.pl @ 13:346a2b0979ea

Adjusted tool definition and wrapper to Flexbar 2.31 release.

--- a/flexbar.pl	Thu Jan 17 18:09:44 2013 +0100
+++ b/flexbar.pl	Thu Jan 17 18:26:14 2013 +0100
@@ -1,24 +1,25 @@
 #!/usr/bin/env perl
 
-# Author: Johannes T. Roehr
+# Flexbar wrapper for Galaxy tool definition, version 2.31
+# 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 reads > '. $outFile and exit 1;
+system $call .' --target FlexbarTargetFile > '. $outFile and exit 1;
 
 
-foreach(<reads*>){
+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 = $_;