--- a/samtools_split.xml	Tue May 09 11:18:30 2017 -0400
+++ b/samtools_split.xml	Mon Jul 29 08:49:33 2019 -0400
@@ -7,13 +7,15 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        samtools split -f 'Read_Group_%!.bam'
-        #if $header:
-            -u '${output}:${header}'
-        #else:
-            -u '${output}'
-        #end if
-        "${input_bam}"
+    @ADDTHREADS@
+    samtools split -f 'Read_Group_%!.bam'
+    #if $header:
+        -u '${output}:${header}'
+    #else:
+        -u '${output}'
+    #end if
+    -@ \$addthreads
+    '$input_bam'
     ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file" />
@@ -21,13 +23,13 @@
      </inputs>
     <outputs>
         <data name="output" format="bam" label="${tool.name} on ${on_string}">
-            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
+            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/>
         </data>
     </outputs>
     <tests>
         <test>
             <param name="input_bam" value="phiX.bam" ftype="bam" />
-            <output name="output" file="samtools_split_out.bam">
+            <output name="output">
                 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
                 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
                 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />