--- a/IsobaricAnalyzer.xml	Thu Jan 11 17:43:42 2018 -0500
+++ b/IsobaricAnalyzer.xml	Mon Feb 12 12:53:14 2018 -0500
@@ -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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Quantitation]-->
-<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0">
+<tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.3.0">
   <description>Calculates isobaric quantitative values for peptides</description>
   <macros>
     <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
@@ -184,6 +184,58 @@
     #end if
   #end for
 #end if
+#if $param_tmt11plex_channel_126_description:
+  -tmt11plex:channel_126_description     "$param_tmt11plex_channel_126_description"
+#end if
+#if $param_tmt11plex_channel_127N_description:
+  -tmt11plex:channel_127N_description     "$param_tmt11plex_channel_127N_description"
+#end if
+#if $param_tmt11plex_channel_127C_description:
+  -tmt11plex:channel_127C_description     "$param_tmt11plex_channel_127C_description"
+#end if
+#if $param_tmt11plex_channel_128N_description:
+  -tmt11plex:channel_128N_description     "$param_tmt11plex_channel_128N_description"
+#end if
+#if $param_tmt11plex_channel_128C_description:
+  -tmt11plex:channel_128C_description     "$param_tmt11plex_channel_128C_description"
+#end if
+#if $param_tmt11plex_channel_129N_description:
+  -tmt11plex:channel_129N_description     "$param_tmt11plex_channel_129N_description"
+#end if
+#if $param_tmt11plex_channel_129C_description:
+  -tmt11plex:channel_129C_description     "$param_tmt11plex_channel_129C_description"
+#end if
+#if $param_tmt11plex_channel_130N_description:
+  -tmt11plex:channel_130N_description     "$param_tmt11plex_channel_130N_description"
+#end if
+#if $param_tmt11plex_channel_130C_description:
+  -tmt11plex:channel_130C_description     "$param_tmt11plex_channel_130C_description"
+#end if
+#if $param_tmt11plex_channel_131N_description:
+  -tmt11plex:channel_131N_description     "$param_tmt11plex_channel_131N_description"
+#end if
+#if $param_tmt11plex_channel_131C_description:
+  -tmt11plex:channel_131C_description     "$param_tmt11plex_channel_131C_description"
+#end if
+#if $param_tmt11plex_reference_channel:
+  -tmt11plex:reference_channel
+  #if " " in str($param_tmt11plex_reference_channel):
+    "$param_tmt11plex_reference_channel"
+  #else
+    $param_tmt11plex_reference_channel
+  #end if
+#end if
+
+#if $rep_param_tmt11plex_correction_matrix:
+-tmt11plex:correction_matrix
+  #for token in $rep_param_tmt11plex_correction_matrix:
+    #if " " in str(token):
+      "$token.param_tmt11plex_correction_matrix"
+    #else
+      $token.param_tmt11plex_correction_matrix
+    #end if
+  #end for
+#end if
 #if $param_tmt6plex_channel_126_description:
   -tmt6plex:channel_126_description     "$param_tmt6plex_channel_126_description"
 #end if
@@ -234,14 +286,15 @@
 #end if
 </command>
   <inputs>
-    <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
+    <param name="param_type" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
       <option value="itraq4plex" selected="true">itraq4plex</option>
       <option value="itraq8plex">itraq8plex</option>
       <option value="tmt10plex">tmt10plex</option>
+      <option value="tmt11plex">tmt11plex</option>
       <option value="tmt6plex">tmt6plex</option>
     </param>
     <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
-    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)">
+    <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use share/OpenMS/IDPool/IDPool.txt)">
       <sanitizer>
         <valid initial="string.printable">
           <remove value="'"/>
@@ -498,6 +551,117 @@
         </sanitizer>
       </param>
     </repeat>
+    <param name="param_tmt11plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_131N_description" type="text" size="30" label="Description for the content of the 131N channel" help="(-channel_131N_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_channel_131C_description" type="text" size="30" label="Description for the content of the 131C channel" help="(-channel_131C_description) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_tmt11plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="(-reference_channel) ">
+      <option value="126" selected="true">126</option>
+      <option value="127N">127N</option>
+      <option value="127C">127C</option>
+      <option value="128N">128N</option>
+      <option value="128C">128C</option>
+      <option value="129N">129N</option>
+      <option value="129C">129C</option>
+      <option value="130N">130N</option>
+      <option value="130C">130C</option>
+      <option value="131N">131N</option>
+      <option value="131C">131C</option>
+    </param>
+    <repeat name="rep_param_tmt11plex_correction_matrix" min="0" max="1" title="param_tmt11plex_correction_matrix">
+      <param name="param_tmt11plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
     <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
       <sanitizer>
         <valid initial="string.printable">