# HG changeset patch
# User jtilman
# Date 1358443574 -3600
# Node ID 346a2b0979ea47ac783cca1767468ff8bb3aa7bc
# Parent  4cbf6c6d2f2b71c9c4ca02e25457f1132c9126f9
Adjusted tool definition and wrapper to Flexbar 2.31 release.

diff -r 4cbf6c6d2f2b -r 346a2b0979ea flexbar.pl
--- 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 = $_;
diff -r 4cbf6c6d2f2b -r 346a2b0979ea flexbar.xml
--- 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