--- a/OpenSwathMzMLFileCacher.xml	Wed Mar 01 12:51:06 2017 -0500
+++ b/OpenSwathMzMLFileCacher.xml	Wed Aug 09 09:47:55 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
-<!--Proposed Tool Section: []-->
-<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.1.0">
+<!--Proposed Tool Section: [Targeted Experiments]-->
+<tool id="OpenSwathMzMLFileCacher" name="OpenSwathMzMLFileCacher" version="2.2.0">
   <description>This tool caches the spectra and chromatogram data of an mzML to disk.</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathMzMLFileCacher</token>
@@ -18,6 +18,14 @@
 #if $param_out:
   -out $param_out
 #end if
+#if $param_out_type:
+  -out_type
+  #if " " in str($param_out_type):
+    "$param_out_type"
+  #else
+    $param_out_type
+  #end if
+#end if
 #if $param_convert_back:
   -convert_back
 #end if
@@ -28,17 +36,21 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mzml" optional="False" label="transition file ('csv')" help="(-in) "/>
+    <param name="param_in" type="data" format="mzml,sqMass" optional="False" label="Input mzML file" help="(-in) "/>
+    <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
+      <option value="mzML">mzML</option>
+      <option value="sqMass">sqMass</option>
+    </param>
     <param name="param_convert_back" display="radio" type="boolean" truevalue="-convert_back" falsevalue="" checked="false" optional="True" label="Convert back to mzML" help="(-convert_back) "/>
     <expand macro="advanced_options">
       <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out" format="data"/>
+    <data name="param_out" format="mzml"/>
   </outputs>
   <help>This tool caches the spectra and chromatogram data of an mzML to disk.
 
 
-For more information, visit </help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathMzMLFileCacher.html</help>
 </tool>