--- a/raceid_clustering.xml	Mon Apr 15 17:54:40 2019 -0400
+++ b/raceid_clustering.xml	Mon Aug 12 13:00:12 2019 -0400
@@ -1,27 +1,12 @@
-<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_PACKAGE@.1" >
+<tool id="raceid_clustering" name="Clustering using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" >
     <description>performs clustering, outlier detection, dimensional reduction</description>
     <macros>
         <import>macros.xml</import>
-        <import>macros_cluster.xml</import>
+        <import>macros_cheetah.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command><![CDATA[
-Rscript '$__tool_directory__/scripts/cluster.R' @GET_VERSION@
-]]></version_command>
-
-    <command detect_errors="exit_code"><![CDATA[
-#set bin = 'cluster.R'
-Rscript '$__tool_directory__/scripts/$bin' '$userconf' 2>&1 > '$outlog'
-    ]]></command>
+    <expand macro="version_command_config" prog="cluster.R" cheetah="CLUSTER_CHEETAH" out="&#38;&#62; '$outlog'" />
 
-    <configfiles>
-        <configfile name="userconf" ><![CDATA[
-@STRING2VECTOR@
-
-@CLUSTER_CHEETAH@
-
-]]></configfile>
-    </configfiles>
     <inputs>
         <param name="inputrds" type="data" format="rdata" label="Input RaceID RDS" help="Requires the RDS output from the normalisation stage" />
         <section name="clust" title="Clustering" expanded="true" >
@@ -90,18 +75,23 @@
     <outputs>
         <data name="outpdf" format="pdf" label="${tool.name} on ${on_string}: PDF Report" />
         <data name="outrdat" format="rdata" label="${tool.name} on ${on_string}: RDS" />
+        <data name="outassignments" format="tabular" label="${tool.name} on ${on_string}: Cell-to-Cluster assignments" />
         <data name="outgenelist" format="tabular" label="${tool.name} on ${on_string}: Cluster - Genes per Cluster" />
         <data name="outlog" format="txt" label="${tool.name} on ${on_string}: Log" >
             <filter>use_log</filter>
         </data>
     </outputs>
-
     <tests>
         <test>
             <param name="inputrds" value="matrix.filter.rdat" />
             <output name="outgenelist" value="matrix2.genelist" />
             <output name="outrdat" value="matrix2.rdat" compare="sim_size" delta="15" />
             <output name="outpdf" value="matrix2.pdf" compare="sim_size" delta="10" />
+            <output name="outassignments" >
+                <assert_contents>
+                    <has_line_matching expression="P1_B1_ATCCAC\s1\s1\sFALSE" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <!-- defaults, but manually specified. No opts, no CC. Generates identical to above -->