--- a/MzMLSplitter.xml	Mon Feb 12 13:12:58 2018 -0500
+++ b/MzMLSplitter.xml	Tue Mar 20 15:23:48 2018 -0400
@@ -7,16 +7,20 @@
     <token name="@EXECUTABLE@">MzMLSplitter</token>
     <import>macros.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MzMLSplitter
+  <command><![CDATA[
+mkdir parts/ &&
+
+MzMLSplitter
 
 #if $param_in:
   -in $param_in
 #end if
 #if $param_out:
-  -out     "$param_out"
+  -out "parts/$param_out"
+#else
+  -out "parts/MzML"
 #end if
 #if $param_parts:
   -parts $param_parts
@@ -43,8 +47,8 @@
   -force
 #end if
 #end if
-&gt; $param_stdout
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
     <param name="param_out" type="text" size="30" label="Prefix for output files ('_part1of2.mzML' etc" help="(-out) will be appended; default: same as 'in' without the file extension)">
@@ -69,10 +73,23 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_stdout" format="txt" label="Output from stdout"/>
+    <collection name="parts" type="list">
+      <discover_datasets pattern="__name_and_ext__" format="mzml"  directory="parts" />
+    </collection>
   </outputs>
+  <tests>
+    <test>
+      <param name="param_in" value="FileFilter_1_input.mzML"/>
+      <param name="param_parts" value="2" />
+      <output_collection name="parts" type="list">
+        <element name="MzML_part1of2" file="MzMLSplitter_output_part1.mzML" ftype="mzml" />
+        <element name="MzML_part2of2" file="MzMLSplitter_output_part2.mzML" ftype="mzml" />
+      </output_collection>
+    </test>
+  </tests>
   <help>Splits an mzML file into multiple parts
 
 
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MzMLSplitter.html</help>
+<expand macro="references"/>
 </tool>