--- a/fastx_barcode_splitter.xml	Fri Nov 08 09:53:39 2013 -0500
+++ b/fastx_barcode_splitter.xml	Tue Oct 27 11:47:52 2015 -0400
@@ -1,59 +1,60 @@
 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
 	<description></description>
-	<command interpreter="bash">
-		fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial 
-		#if $refBarcodeLocation.barcodeLocation == "idxfile":
-		  --idxfile $refBarcodeLocation.idxfile 
-		#else: 
-		  $refBarcodeLocation.EOL 
-		#end if
-		> $output
+	<command interpreter="bash"><![CDATA[
+fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial
+#if $refBarcodeLocation.barcodeLocation == "idxfile":
+    --idxfile $refBarcodeLocation.idxfile
+#else:
+    $refBarcodeLocation.EOL
+#end if
+> $output
+]]>
 	</command>
 
 	<inputs>
-		<param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" />
-		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" />
+		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
+		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 
 		<conditional name="refBarcodeLocation">
-			<param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at">
+			<param name="barcodeLocation" type="select" label="Barcodes found at">
 				<option value="bol">Start of sequence (5' end)</option>
 				<option value="eol">End of sequence (3' end)</option>
 				<option value="idxfile">Separate index file</option>
 			</param>
 			<when value="bol">
-				<param version="1.1" name="EOL" type="hidden" value="--bol" />
+				<param name="EOL" type="hidden" value="--bol" />
 			</when>
 			<when value="eol">
-				<param version="1.1" name="EOL" type="hidden" value="--eol" />
+				<param name="EOL" type="hidden" value="--eol" />
 			</when>
 			<when value="idxfile">
-				<param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
+				<param name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
 			</when>
 		</conditional>
 
-		<param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
-		
-		<param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
-	
+		<param name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
+
+		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
+
 	</inputs>
-	
-	<tests>
+
+	<outputs>
+		<data format="html" name="output" />
+	</outputs>
+
+    <tests>
 		<test>
 			<!-- Split a FASTQ file -->
-			<param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" />
-			<param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
-			<param version="1.1" name="EOL" value="Start of sequence (5' end)" />
-			<param version="1.1" name="mismatches" value="2" />
-			<param version="1.1" name="partial" value="0" />
-			<output version="1.1" name="output" file="fastx_barcode_splitter1.out" />
+			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
+			<param name="barcodeLocation" value="bol" />
+			<param name="mismatches" value="2" />
+			<param name="partial" value="0" />
+			<output name="output" file="fastx_barcode_splitter1.out" />
 		</test>
 	</tests>
 
-	<outputs>
-		<data version="1.1" format="html" name="output" />
-	</outputs>
-<help>
-
+    <help><![CDATA[
 **What it does**
 
 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
@@ -71,7 +72,7 @@
     BC2	ATCGT
     BC3	GTGAT
     BC4 TGTCT
-    
+
 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
 Sequences matching the barcode will be stored in the appropriate file.
 
@@ -79,14 +80,18 @@
 
 The output of this tool is an HTML file, displaying the split counts and the file names.
 In addition, each fastq file produced will be loaded into the galaxy history automatically.
-
-
-------
-
-This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
+]]>
+	</help>
 
- .. __: http://hannonlab.cshl.edu/fastx_toolkit/
- 
-</help>
-<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+	<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
+	<citations>
+	    <citation type="bibtex">
+			@misc{gordon_fastx-toolkit_????,
+				title = {{FASTX}-{Toolkit}},
+				url = {http://hannonlab.cshl.edu/fastx_toolkit/index.html},
+				author = {Gordon, Assaf}
+			}
+		</citation>
+	</citations>
+
 </tool>