--- a/flexbar.xml	Thu Jan 17 18:09:44 2013 +0100
+++ b/flexbar.xml	Thu Jan 17 18:26:14 2013 +0100
@@ -1,12 +1,13 @@
 
-<!-- Author: Johannes T. Roehr -->
+<!-- Flexbar tool definition for Galaxy, version 2.31 -->
+<!-- Author: Johannes Roehr -->
 
-<tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True">
+<tool id="flexbar" name="Flexbar" version="2.31" force_history_refresh="True">
 
 	<description>flexible barcode and adapter removal</description>
     
 	<requirements>
-        <requirement type="binary" version="2.3">flexbar</requirement>
+        <requirement type="binary" version="2.31">flexbar</requirement>
     </requirements>
 	
 	<version_command>flexbar --version</version_command>
@@ -126,12 +127,11 @@
 		
 		#if $cLogging.select == "show":
 			$cLogging.logLevel
-			$cLogging.noLenDist
-			$cLogging.remTag
-		#end if
-		
-		#if $cLogging.select == "off":
-			--no-length-dist
+			$cLogging.singleReads
+			$cLogging.lenDist
+			$cLogging.fastaOutput
+			$cLogging.numTags
+			$cLogging.remTags
 		#end if
 		
 		
@@ -330,19 +330,34 @@
 					<option value="--log-level MOD">Modified</option>
 					<option value="--log-level TAB">Tabular</option>
 				</param>
-			
-				<param name="noLenDist" type="select" label="Read length distribution">
-					<option value="--no-length-dist" selected="true">Off</option>
-					<option value="">On</option>
+				
+				<param name="singleReads" type="select" label="Single reads">
+					<option value="" selected="true">Off</option>
+					<option value="--single-reads">On</option>
+				</param>
+				
+				<param name="lenDist" type="select" label="Read length distribution">
+					<option value="" selected="true">Off</option>
+					<option value="--length-dist">On</option>
 				</param>
-		
-				<param name="remTag" type="select" label="Read tagging">
+				
+				<param name="fastaOutput" type="select" label="Fasta output">
 					<option value="" selected="true">Off</option>
-					<option value="--removal-tag">Removal tags</option>
+					<option value="--fasta-output">Always</option>
+				</param>
+				
+				<param name="numTags" type="select" label="Number tags">
+					<option value="" selected="true">Off</option>
+					<option value="--number-tags">On</option>
+				</param>
+				
+				<param name="remTags" type="select" label="Removal tags">
+					<option value="" selected="true">Off</option>
+					<option value="--removal-tags">On</option>
 				</param>
 			</when>
 		</conditional>
-
+		
   	</inputs>
  	
 	<stdio>
@@ -351,11 +366,12 @@
 	
 	<outputs>
 	    <data format="txt" name="output" metadata_source="reads"/>
-	  </outputs>
+	</outputs>
 	
 	
 	<help>
-**Flexbar help**
+
+**Flexbar description**
 
 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
 
@@ -363,12 +379,6 @@
 
 ------
 
-**Reference**
-
-Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
-
-------
-
 **Trim-end modes**
 
 **Any:** longer part of read remains
@@ -383,6 +393,12 @@
 
 ------
 
+**Reference**
+
+Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
+
+------
+
 **Documentation**
 
 .. class:: warningmark