--- a/MapAlignerPoseClustering.xml	Mon Feb 12 10:28:56 2018 -0500
+++ b/MapAlignerPoseClustering.xml	Mon Feb 12 12:57:02 2018 -0500
@@ -1,9 +1,13 @@
-<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0">
+<?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 CTDConverter.-->
+<!--Proposed Tool Section: [Map Alignment]-->
+<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0">
   <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
   <macros>
     <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
     <import>macros.xml</import>
   </macros>
+  <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
   <command><![CDATA[
@@ -26,8 +30,6 @@
     ./results_trafoxml/${infile.element_identifier}.trafoxml
 #end for
 
--threads "\${GALAXY_SLOTS:-1}"
-
 #if $param_reference_file:
   -reference:file $param_reference_file
 #end if
@@ -73,7 +75,9 @@
   #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
-
+    #if $adv_opts.param_force:
+  -force
+#end if
     #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction:
   -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction
 #end if
@@ -83,8 +87,13 @@
     #if $adv_opts.param_algorithm_superimposer_max_scaling:
   -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling
 #end if
-
-#if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
+    #if $adv_opts.param_algorithm_superimposer_dump_buckets:
+  -algorithm:superimposer:dump_buckets     "$adv_opts.param_algorithm_superimposer_dump_buckets"
+#end if
+    #if $adv_opts.param_algorithm_superimposer_dump_pairs:
+  -algorithm:superimposer:dump_pairs     "$adv_opts.param_algorithm_superimposer_dump_pairs"
+#end if
+    #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent:
   -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent
 #end if
     #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight:
@@ -111,7 +120,6 @@
   #end if
 #end if
 #end if
-
  ]]>
 </command>
   <inputs>
@@ -133,9 +141,26 @@
       <option value="ppm">ppm</option>
     </param>
     <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_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction)  "/>
       <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift)  This applies for both directions"/>
       <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling)  The minimal scaling is the reciprocal of this"/>
+      <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets)  A serial number for each invocation will be appended automatically">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+      <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs)  A serial number for each invocation will be appended automatically">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
       <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
       <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/>
       <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
@@ -159,6 +184,5 @@
     </outputs>
     <help>Corrects retention time distortions between maps using a pose clustering approach.
 
-
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
 </tool>