# HG changeset patch
# User jtilman
# Date 1529416737 14400
# Node ID d43903772a88a096efb00274673b56f98d81eba5
# Parent  18acb52de258769ff74f1c9829fc934270cb1ae5
Uploaded

diff -r 18acb52de258 -r d43903772a88 flexbar.xml
--- a/flexbar.xml	Tue Jun 05 11:47:53 2018 -0400
+++ b/flexbar.xml	Tue Jun 19 09:58:57 2018 -0400
@@ -1,17 +1,17 @@
 
-<!-- Flexbar tool definition for Galaxy, version 2.5 -->
+<!-- Flexbar tool definition for Galaxy, version 3.4 -->
 <!-- Author: Johannes Roehr -->
 
 
-<tool id="flexbar" name="Flexbar" version="2.5" force_history_refresh="True">
+<tool id="flexbar" name="Flexbar" version="3.4" force_history_refresh="True">
 	
 	<description>flexible barcode and adapter removal</description>
     
 	<requirements>
-        <requirement type="binary" version="2.5">flexbar</requirement>
+        <requirement type="binary" version="3.4">flexbar</requirement>
     </requirements>
 	
-	<version_command>flexbar --version</version_command>
+	<version_command>flexbar --versions</version_command>
 	
 	<command interpreter="perl">
 		
@@ -27,23 +27,6 @@
 			#end if
 		#end if
 		
-		#if $reads.ext == "fastqsanger":
-			--format sanger
-		#end if
-		#if $reads.ext == "fastqsolexa":
-			--format solexa
-		#end if
-		#if $reads.ext == "fastqillumina":
-			--format i1.3
-		#end if
-		#if $reads.ext == "csfasta":
-			--color-space
-		#end if
-		#if $reads.ext == "fastqcssanger":
-			--color-space
-		#end if
-		
-		
 		--max-uncalled $maxUncalled
 		--min-read-length $minReadLen
 		
@@ -53,7 +36,17 @@
 		#end if
 		
 		#if $cTrimPhred.select == "on":
-			--pre-trim-phred $cTrimPhred.trimPhred
+			--qtrim TAIL --qtrim-threshold $cTrimPhred.trimPhred
+			
+			#if $reads.ext == "fastqsanger":
+				--qtrim-format sanger
+			#end if
+			#if $reads.ext == "fastqsolexa":
+				--qtrim-format solexa
+			#end if
+			#if $reads.ext == "fastqillumina":
+				--qtrim-format i1.3
+			#end if
 		#end if
 		
 		#if $cTrimLen.select == "on":
@@ -84,7 +77,7 @@
 				--barcode-min-overlap $cBarcodes.cbMinOverlap.bMinOverlap
 			#end if
 			
-			--barcode-threshold $cBarcodes.bThresh
+			--barcode-error-rate $cBarcodes.bThresh
 			
 			#if $cBarcodes.cbAlignScores.select == "yes":
 				--barcode-match    $bMatch
@@ -113,7 +106,7 @@
 			$cAdapters.aReadSet
 			
 			--adapter-min-overlap $cAdapters.aMinOverlap
-			--adapter-threshold   $cAdapters.aThresh
+			--adapter-error-rate  $cAdapters.aThresh
 			
 			#if $cAdapters.caAlignScores.select == "yes":
 				--adapter-match    $aMatch
@@ -144,18 +137,18 @@
 	
 	<inputs>
 		
-		<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads" type="data" label="Sequencing reads" optional="false"/>
+		<param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data" label="Reads fastq file" optional="false"/>
 		
 		
 		<conditional name="cReads2">
-			<param name="select" type="select" label="2nd read set (paired)">
+			<param name="select" type="select" label="Paired reads file">
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
 			<when value="off">
 			</when>
 			<when value="on">
-				<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
+				<param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="reads2" type="data" label="Reads 2" optional="false" help="same format as first read set"/>
 			</when>
 		</conditional>
 		
@@ -176,7 +169,7 @@
 		</conditional>
 		
 		<conditional name="cTrimPhred">
-			<param name="select" type="select" label="3) Phred-trimming">
+			<param name="select" type="select" label="3) Quality-based trimming">
 				<option value="off" selected="true">Off</option>
 				<option value="on">On</option>
 			</param>
@@ -204,7 +197,7 @@
 						<option value="yes">Yes</option>
 					</param>
 					<when value="yes">
-						<param format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina,csfasta,fastqcssanger" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
+						<param format="fastq,fastqsanger,fastqsolexa,fastqillumina" name="bReads" type="data" label="Separate barcode reads" optional="false"/>
 					</when>
 					<when value="no">
 						<param name="bKeep" type="select" label="Remove barcodes within reads">
@@ -222,9 +215,9 @@
 				<param name="bTrimEnd" type="select" label="Trim-end mode" optional="false">
 					<option value="ANY" selected="true">Any</option>
 					<option value="RIGHT">Right</option>
-					<option value="RIGHT_TAIL">Right tail</option>
+					<option value="RTAIL">Right tail</option>
 					<option value="LEFT">Left</option>
-					<option value="LEFT_TAIL">Left tail</option>
+					<option value="LTAIL">Left tail</option>
 				</param>
 				
 				<conditional name="cbTailLen">
@@ -299,9 +292,9 @@
 				<param name="aTrimEnd" type="select" label="Trim-end mode" optional="false">
 					<option value="ANY">Any</option>
 					<option value="RIGHT" selected="true">Right</option>
-					<option value="RIGHT_TAIL">Right tail</option>
+					<option value="RTAIL">Right tail</option>
 					<option value="LEFT">Left</option>
-					<option value="LEFT_TAIL">Left tail</option>
+					<option value="LTAIL">Left tail</option>
 				</param>
 				
 				<conditional name="caTailLen">
@@ -335,7 +328,7 @@
 					<when value="yes">
 						<param name="aMatch"    size="3" type="integer" value="1"  label="Match" optional="false"/>
 						<param name="aMismatch" size="3" type="integer" value="-1" label="Mismatch" optional="false"/>
-						<param name="aGap"      size="3" type="integer" value="-7" label="Gap" optional="false"/>
+						<param name="aGap"      size="3" type="integer" value="-6" label="Gap" optional="false"/>
 					</when>
 				</conditional>
 			</when>
@@ -391,9 +384,9 @@
 			<when value="show">
 				<param name="logLevel" type="select" label="Alignment logging">
 					<option value="" selected="true">Off</option>
-					<option value="--log-level ALL">All</option>
-					<option value="--log-level MOD">Modified</option>
-					<option value="--log-level TAB">Tabular</option>
+					<option value="--align-log ALL">All</option>
+					<option value="--align-log MOD">Modified</option>
+					<option value="--align-log TAB">Tabular</option>
 				</param>
 				
 				<param name="numTags" type="select" label="Number tags">
@@ -406,9 +399,9 @@
 					<option value="--removal-tags">On</option>
 				</param>
 				
-				<param name="rndTags" type="select" label="Random tags">
+				<param name="rndTags" type="select" label="UMI tags">
 					<option value="" selected="true">Off</option>
-					<option value="--random-tags">On</option>
+					<option value="--umi-tags">On</option>
 				</param>
 			</when>
 		</conditional>
@@ -428,7 +421,7 @@
 
 **Description**
 
-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.
+The program 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 as well as transcriptome assemblies. Unique molecular identifiers can be extracted in a flexible way. The program supports sequencing data in fastq format, e.g. from the Illumina platform. Flexbar is available on the project_ page.
 
 .. _project: https://github.com/seqan/flexbar
 
@@ -450,15 +443,19 @@
 
 **Documentation**
 
-Further documentation is available on the `manual`__ wiki page and via the command line help screen.
+Further documentation is available on the `manual`__ page and via the command line help screen.
 
 .. __: https://github.com/seqan/flexbar/wiki
 
 ------
 
-**Reference**
+**References**
 
-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.
+Johannes T. Roehr, Christoph Dieterich, Knut Reinert:  
+Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics 2017.
+
+Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich:  
+Flexbar – flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012.
 
 	</help>