--- a/fastq-join.xml	Fri Jun 27 15:39:38 2014 -0400
+++ b/fastq-join.xml	Mon Jul 13 11:45:19 2015 -0400
@@ -1,10 +1,16 @@
-<tool id="fastq_join" name="fastq-join" version="1.1.2-484">
-    <description> - Joins paired-end reads on the overlapping ends</description>
+<tool id="fastq_join" name="fastq-join" version="0.1.1">
+    <description> - Joins two paired-end reads on the overlapping ends</description>
+
     <requirements>
         <requirement type="package" version="1.1.2-484">ea-utils</requirement>
     </requirements>
-    <command>
-        fastq-join 
+
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
+    </stdio>
+
+    <command><![CDATA[
+        fastq-join
         -v '$splitChar'
         -p $pctMaxDiff
         -m $minOverlap
@@ -13,8 +19,10 @@
         #end if
         $read1
         $read2
-        -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined 
+        -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined
+        ]]>
     </command>
+
     <inputs>
         <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" />
         <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" />
@@ -25,18 +33,14 @@
     </inputs>
 
     <outputs>
-        <data format="input" format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
-        <data format="input" format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
-        <data format="input" format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
+        <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/>
+        <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/>
+        <data format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/>
         <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)">
             <filter>stitchLengthReport</filter>
         </data>
     </outputs>
 
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
-    </stdio>
-
     <tests>
         <test>
             <param name="read1" value="test_read1.fastq" />
@@ -47,7 +51,7 @@
         </test>
     </tests>
 
-    <help>
+    <help><![CDATA[
 Overview
 --------
 fastq-join joins two paired-end reads on the overlapping ends.
@@ -61,5 +65,27 @@
 Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was.
 
 This tool uses sqr(distance)/len for anchored alignment quality algorithm. It's a good measure of anchored alignment quality, akin to squared-deviation for means.  This tool uses the fastq-join program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/FastqJoin for details.
+]]>
     </help>
+
+    <citations>
+        <citation type="bibtex">
+            @article{aronesty_comparison_2013,
+                title = {Comparison of {Sequencing} {Utility} {Programs}},
+                volume = {7},
+                issn = {18750362},
+                url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
+                doi = {10.2174/1875036201307010001},
+                language = {en},
+                number = {1},
+                urldate = {2015-07-10},
+                journal = {The Open Bioinformatics Journal},
+                author = {Aronesty, Erik},
+                month = jan,
+                year = {2013},
+                pages = {1--8}
+            }
+        </citation>
+    </citations>
+
 </tool>