--- a/je	Tue Aug 01 03:42:23 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#!/bin/sh
-# Wrapper around je_1.1_bundle.jar
-
-# where are we stored ?
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-# echo $DIR
-# path to jar file to execute, this jar is supposed to be in the same dir as this script
-JAR_FILE=$DIR"/je_1.2_bundle.jar"
-
-# set default _JAVA_OPTIONS
-_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'}
-export _JAVA_OPTIONS
-
-# uncomment to change logging level using your own log4j.xml found in $DIR file
-# OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml"
-
-java $OPTS -jar $JAR_FILE "$@"
-exit $?

--- a/je-demultiplex-illu.xml	Tue Aug 01 03:42:23 2017 -0400
+++ b/je-demultiplex-illu.xml	Wed Aug 02 10:59:09 2017 -0400
@@ -3,11 +3,12 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
     </stdio>
-    <version_command>echo '1.0'</version_command>
-    <command interpreter="bash">
+    <expand macro="version_command" />
+    <command>
 <![CDATA[
     je demultiplex-illu
 
@@ -93,7 +94,7 @@
             <param name="MM" value="3"/>
             <param name="MMD" value="2"/>
             <param name="Q" value="20"/>
-	    <param name="DIAG" value="false"/>
+	        <param name="DIAG" value="false"/>
             <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4">
                 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
                 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
@@ -111,8 +112,7 @@
         </test>
     </tests>
 
-
-  <help>
+    <help>
 <![CDATA[
 **What it does**
 
@@ -423,6 +423,6 @@
 
     Default value: null.
 ]]>
-  </help>
-
+    </help>
+    <expand macro="citations"/>
 </tool>

Binary file je_1.2_bundle.jar has changed

--- a/macros.xml	Tue Aug 01 03:42:23 2017 -0400
+++ b/macros.xml	Wed Aug 02 10:59:09 2017 -0400
@@ -1,6 +1,14 @@
 <macros>
 
     <token name="@VERSION_STRING@">1.2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">je-suite</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>je version 2&gt;&amp;1 | tail -n 1</version_command>
+    </xml>
 
     <token name="@single_or_paired_cmd@">
         #if str( $library.type ) == "single":
@@ -278,7 +286,7 @@
     </token>
     <xml name="demultiplexer_common_output_options">
         <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
-            truealue="true"
+            truevalue="true"
             falsevalue="false"
             checked="true"
         />
@@ -317,11 +325,9 @@
             help="Set to empty or null for no replacement."
             value=":"/>
 
-        <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"
+        <param name="GZ" type="hidden" label="Compress output (GZ)"
             help="will result in fastq.gz files."
-            truevalue="true"
-            falsevalue="false"
-            checked="false"/>
+            value="false"/>
     </xml>
 
     <token name="@demultiplexer_common_outputs_cmd@">
@@ -336,5 +342,9 @@
             <filter>(adv_options['DIAG'] == 'true')</filter>
         </data>
     </xml>
-
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s12859-016-1284-2</citation>
+        </citations>
+    </xml>
 </macros>