--- a/FeatureLinkerUnlabeledQT.xml	Thu Apr 27 13:21:12 2017 -0400
+++ b/FeatureLinkerUnlabeledQT.xml	Wed Aug 09 09:10:00 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: [Map Alignment]-->
-<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.1.0">
+<tool id="FeatureLinkerUnlabeledQT" name="FeatureLinkerUnlabeledQT" version="2.2.0">
   <description>Groups corresponding features from multiple maps.</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureLinkerUnlabeledQT</token>
@@ -67,6 +67,14 @@
     #if $adv_opts.param_algorithm_distance_intensity_weight:
   -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight
 #end if
+    #if $adv_opts.param_algorithm_distance_intensity_log_transform:
+  -algorithm:distance_intensity:log_transform
+  #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform):
+    "$adv_opts.param_algorithm_distance_intensity_log_transform"
+  #else
+    $adv_opts.param_algorithm_distance_intensity_log_transform
+  #end if
+#end if
 #end if
 </command>
   <inputs>
@@ -80,7 +88,7 @@
     </param>
     <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/>
     <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)" help="(-use_identifications) "/>
-    <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="1" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help="(-nr_partitions) "/>
+    <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="How many partitions in m/z space should be used for the algorithm (more partitions means faster runtime and more memory efficient execution )" help="(-nr_partitions) "/>
     <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/>
     <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/>
     <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/>
@@ -96,6 +104,10 @@
       <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/>
       <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/>
       <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/>
+      <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))">
+        <option value="enabled">enabled</option>
+        <option value="disabled" selected="true">disabled</option>
+      </param>
     </expand>
   </inputs>
   <outputs>