# HG changeset patch
# User jtilman
# Date 1375800573 -7200
# Node ID 12e4b3bb38c68e7015a0d13570ccc0a6250a498c
# Parent  d62311a7bac65f8cec247dc1d7e0a50949dfb796
Adjusted tool definition to Flexbar release 2.4

diff -r d62311a7bac6 -r 12e4b3bb38c6 flexbar.pl
--- a/flexbar.pl	Thu May 23 20:51:05 2013 +0200
+++ b/flexbar.pl	Tue Aug 06 16:49:33 2013 +0200
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Flexbar wrapper for Galaxy tool definition, version 2.34
+# Flexbar wrapper for Galaxy tool definition, version 2.4
 # Author: Johannes Roehr
 
 use warnings;
@@ -20,11 +20,12 @@
 	$fileType = $1         if /\.(\w+)$/;
 	$fileType = $format    if /\.\w*fast\w$/;
 	$fileType = 'fasta'    if /\.fasta$/;
-	$fileType = 'tabular'  if $fileType eq 'lengthdist';
+	$fileType = 'csfasta'  if /\.csfasta$/;
+	$fileType = 'tabular'  if /\.lengthdist$/;
 	
 	my $file = $_;
 	
-	s/_//g;
+	s/_/-/g;
 	
 	my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
 	
diff -r d62311a7bac6 -r 12e4b3bb38c6 flexbar.xml
--- a/flexbar.xml	Thu May 23 20:51:05 2013 +0200
+++ b/flexbar.xml	Tue Aug 06 16:49:33 2013 +0200
@@ -1,13 +1,14 @@
 
-<!-- Flexbar tool definition for Galaxy, version 2.34 -->
+<!-- Flexbar tool definition for Galaxy, version 2.4 -->
 <!-- Author: Johannes Roehr -->
 
-<tool id="flexbar" name="Flexbar" version="2.34" force_history_refresh="True">
 
+<tool id="flexbar" name="Flexbar" version="2.4" force_history_refresh="True">
+	
 	<description>flexible barcode and adapter removal</description>
     
 	<requirements>
-        <requirement type="binary" version="2.34">flexbar</requirement>
+        <requirement type="binary" version="2.4">flexbar</requirement>
     </requirements>
 	
 	<version_command>flexbar --version</version_command>
@@ -26,32 +27,25 @@
 			#end if
 		#end if
 		
-		
-		#if $reads.ext == "fasta":
-			--format fasta
-		#end if
-		#if $reads.ext == "fastq":
-			--format fastq
-		#end if
 		#if $reads.ext == "fastqsanger":
-			--format fastq-sanger
+			--format sanger
 		#end if
 		#if $reads.ext == "fastqsolexa":
-			--format fastq-solexa
+			--format solexa
 		#end if
 		#if $reads.ext == "fastqillumina":
-			--format fastq-i1.3
+			--format i1.3
 		#end if
 		#if $reads.ext == "csfasta":
-			--format csfasta
+			--color-space
 		#end if
 		#if $reads.ext == "fastqcssanger":
-			--format csfastq
+			--color-space
 		#end if
 		
 		
 		--max-uncalled $maxUncalled
-		--min-readlength $minReadLen
+		--min-read-length $minReadLen
 		
 		#if $trimEnds.select == "on":
 			--pre-trim-left $trimEnds.trimLeft
@@ -78,6 +72,8 @@
 				$cBarcodes.cbReads.bKeep
 			#end if
 			
+			$cBarcodes.bUnassigned
+			
 			--barcode-trim-end $cBarcodes.bTrimEnd
 			
 			#if $cBarcodes.cbTailLen.select == "yes":
@@ -88,7 +84,7 @@
 				--barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
 			#end if
 			
-			--barcode-threshold   $cBarcodes.bThresh
+			--barcode-threshold $cBarcodes.bThresh
 			
 			#if $cBarcodes.cbAlignScores.select == "yes":
 				--barcode-match    $bMatch
@@ -114,6 +110,8 @@
 				--adapter-tail-length $cAdapters.caTailLen.aTailLen
 			#end if
 			
+			$cAdapters.aReadSet
+			
 			--adapter-min-overlap $cAdapters.aMinOverlap
 			--adapter-threshold   $cAdapters.aThresh
 			
@@ -125,11 +123,14 @@
 		#end if
 		
 		
+		#if $cOutput.select == "show":
+			$cOutput.fastaOutput
+			$cOutput.lenDist
+			$cOutput.singleReads
+		#end if
+		
 		#if $cLogging.select == "show":
 			$cLogging.logLevel
-			$cLogging.singleReads
-			$cLogging.lenDist
-			$cLogging.fastaOutput
 			$cLogging.numTags
 			$cLogging.remTags
 			$cLogging.rndTags
@@ -140,6 +141,7 @@
 		
 	</command>
 	
+	
 	<inputs>
 		
 		<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
@@ -195,6 +197,7 @@
 			</when>
 			<when value="on">
 				<param format="fasta" name="barcodes" type="data" label="Barcodes" optional="false"/>
+				
 				<conditional name="cbReads">
 					<param name="select" type="select" label="Separate barcode reads">
 						<option value="no" selected="true">No</option>
@@ -210,6 +213,12 @@
 						</param>
 					</when>
 				</conditional>
+				
+				<param name="bUnassigned" type="select" label="Include unassigned reads">
+					<option value="" selected="true">No</option>
+					<option value="--barcode-unassigned">Yes</option>
+				</param>
+				
 				<param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
 					<option value="ANY" selected="true">Any</option>
 					<option value="RIGHT">Right</option>
@@ -217,6 +226,7 @@
 					<option value="LEFT">Left</option>
 					<option value="LEFT_TAIL">Left tail</option>
 				</param>
+				
 				<conditional name="cbTailLen">
 					<param name="select" type="select" label="Change tail length">
 						<option value="no" selected="true">No</option>
@@ -253,7 +263,7 @@
 					<when value="yes">
 						<param name="bMatch"    size="3" type="integer" value="1"  label="Match" optional="false"/>
 						<param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
-						<param name="bGap"      size="3" type="integer" value="-7" label="Gap" optional="false"/>
+						<param name="bGap"      size="3" type="integer" value="-9" label="Gap" optional="false"/>
 					</when>
 				</conditional>
 			</when>
@@ -306,6 +316,12 @@
 					</when>
 				</conditional>
 				
+				<param name="aReadSet" type="select" label="Removal for single read set">
+					<option value="" selected="true">No</option>
+					<option value="--adapter-read-set 1">1st</option>
+					<option value="--adapter-read-set 2">2nd</option>
+				</param>
+				
 				<param name="aMinOverlap" size="4" type="integer" value="1" label="Min-overlap" optional="false"/>
 				<param name="aThresh" size="4" type="integer" value="3" label="Threshold" optional="false" help="allowed mismatches and indels per 10 bases"/>
 				
@@ -340,6 +356,30 @@
 		
 		<param name="minReadLen"  size="4" type="integer" value="18" label="7) Minimum read length" optional="false" help="shorter reads are discarded"/>
 		
+		<conditional name="cOutput">
+			<param name="select" type="select" label="Output selection">
+				<option value="off" selected="true">Off</option>
+				<option value="show">Show</option>
+			</param>
+			<when value="off">
+			</when>
+			<when value="show">
+				<param name="fastaOutput" type="select" label="Fasta output">
+					<option value="" selected="true">Off</option>
+					<option value="--fasta-output">Always</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="singleReads" type="select" label="Single reads">
+					<option value="" selected="true">Off</option>
+					<option value="--single-reads">On</option>
+				</param>
+			</when>
+		</conditional>
 		
 		<conditional name="cLogging">
 			<param name="select" type="select" label="Logging and tagging options">
@@ -356,21 +396,6 @@
 					<option value="--log-level TAB">Tabular</option>
 				</param>
 				
-				<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="fastaOutput" type="select" label="Fasta output">
-					<option value="" selected="true">Off</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>
@@ -387,7 +412,7 @@
 				</param>
 			</when>
 		</conditional>
-		
+
 		<param name="threads" type="select" label="Threads" help="check availability of cores">
 		    <option value="1" selected="true">1</option>
 		    <option value="2">2</option>
@@ -409,7 +434,7 @@
 
 **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. Flexbar is available on the project_ page.
+Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read 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. Flexbar is available on the project_ page.
 
 .. _project: https://sourceforge.net/projects/flexbar
 
@@ -417,15 +442,15 @@
 
 **Trim-end modes**
 
-**Any:** longer part of read remains
+**Any:** longer side of read remains after overlap removal
 
-**Left:** align before or at read end, right part remains
+**Left:** right side remains after removal, align before or at read end
 
-**Right:** align after or at read start, left part remains
+**Right:** left part remains after removal, align after or at read start
 
-**Left tail:** consider first n bases, see tail-length options
+**Left tail:** consider first n bases of reads in alignment
 
-**Right tail:** use only last n bases of reads in alignment
+**Right tail:** use only last n bases, see tail-length options
 
 ------