--- a/IDMapper.xml	Thu Apr 27 13:23:39 2017 -0400
+++ b/IDMapper.xml	Wed Aug 09 09:18:09 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: [ID Processing]-->
-<tool id="IDMapper" name="IDMapper" version="2.1.0">
+<tool id="IDMapper" name="IDMapper" version="2.2.0">
   <description>Assigns protein/peptide identifications to features or consensus features.</description>
   <macros>
     <token name="@EXECUTABLE@">IDMapper</token>
@@ -55,6 +55,9 @@
 #if $param_consensus_use_subelements:
   -consensus:use_subelements
 #end if
+#if $param_spectra_in:
+  -spectra:in $param_spectra_in
+#end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
   -force
@@ -81,6 +84,7 @@
     <param name="param_feature_use_centroid_rt" display="radio" type="boolean" truevalue="-feature:use_centroid_rt" falsevalue="" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help="(-use_centroid_rt) "/>
     <param name="param_feature_use_centroid_mz" display="radio" type="boolean" truevalue="-feature:use_centroid_mz" falsevalue="" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(-use_centroid_mz) &lt;br&gt;(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
     <param name="param_consensus_use_subelements" display="radio" type="boolean" truevalue="-consensus:use_subelements" falsevalue="" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="(-use_subelements) A consensus feature matches if any of its sub-features matches"/>
+    <param name="param_spectra_in" type="data" format="mzml" optional="True" label="MS run used to annotated unidentified spectra to features or consensus features" help="(-in) "/>
     <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) "/>
       <param name="param_consensus_annotate_ids_with_subelements" display="radio" type="boolean" truevalue="-consensus:annotate_ids_with_subelements" falsevalue="" checked="false" optional="True" label="Store the map index of the sub-feature in the peptide ID" help="(-annotate_ids_with_subelements) "/>