--- a/HighResPrecursorMassCorrector.xml	Mon Oct 13 10:18:22 2014 -0400
+++ b/HighResPrecursorMassCorrector.xml	Wed Jan 27 10:06:49 2016 -0500
@@ -1,33 +1,101 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="1.12.0">
-  <description>Corrects the precursor mz determined by the instrument software.</description>
-  <macros>
-    <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>HighResPrecursorMassCorrector
+<?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: [Signal processing and preprocessing]-->
+  <tool id="HighResPrecursorMassCorrector" name="HighResPrecursorMassCorrector" version="2.0.0">
+    <description>Corrects the precursor mass and charge determined by the instrument software.</description>
+    <macros>
+      <token name="@EXECUTABLE@">HighResPrecursorMassCorrector</token>
+      <import>macros.xml</import>
+    </macros>
+    <expand macro="references"/>
+    <expand macro="stdio"/>
+    <expand macro="requirements"/>
+    <command>HighResPrecursorMassCorrector
 
--in ${param_in}
--out ${param_out}
--out_csv ${param_out_csv}
--threads \${GALAXY_SLOTS:-24} 
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_out_csv:
+  -out_csv $param_out_csv
+#end if
+-threads \${GALAXY_SLOTS:-24}
+#if $param_feature_in:
+  -feature:in $param_feature_in
+#end if
+#if $param_feature_mz_tolerance:
+  -feature:mz_tolerance $param_feature_mz_tolerance
+#end if
+#if $param_feature_mz_tolerance_unit:
+  -feature:mz_tolerance_unit
+  #if &quot; &quot; in str($param_feature_mz_tolerance_unit):
+    &quot;$param_feature_mz_tolerance_unit&quot;
+  #else
+    $param_feature_mz_tolerance_unit
+  #end if
+#end if
+#if $param_feature_rt_tolerance:
+  -feature:rt_tolerance $param_feature_rt_tolerance
+#end if
+#if $param_feature_believe_charge:
+  -feature:believe_charge
+#end if
+#if $param_feature_keep_original:
+  -feature:keep_original
+#end if
+#if $param_feature_assign_all_matching:
+  -feature:assign_all_matching
+#end if
+#if $param_nearest_peak_mz_tolerance:
+  -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
+#end if
+#if $param_nearest_peak_mz_tolerance_unit:
+  -nearest_peak:mz_tolerance_unit
+  #if &quot; &quot; in str($param_nearest_peak_mz_tolerance_unit):
+    &quot;$param_nearest_peak_mz_tolerance_unit&quot;
+  #else
+    $param_nearest_peak_mz_tolerance_unit
+  #end if
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+    #if $adv_opts.param_feature_max_trace:
+  -feature:max_trace $adv_opts.param_feature_max_trace
+#end if
+#end if
 </command>
-  <inputs>
-    <param name="param_in" type="data" format="mzML" optional="False" label="input file (centroided data)" help="(-in)"/>
-  </inputs>
-  <outputs>
-    <data name="param_out" label="output file" format="mzML"/>
-    <data name="param_out_csv" label="Optional csv output file containing columns: precursor rt, uncorrected mz, corrected mz, delta mz#br#" format="tabular"/>
-  </outputs>
-  <help>**What it does**
-
-Corrects the precursor mz determined by the instrument software.
+    <inputs>
+      <param format="mzml" help="(-in) " label="input file (centroided data)" name="param_in" optional="False" type="data"/>
+      <param format="xml" help="(-in) " label="features used to correct precursor masses" name="param_feature_in" optional="True" type="data"/>
+      <param help="(-mz_tolerance) Used to determine matching to feature mass traces" label="The precursor mass tolerance" name="param_feature_mz_tolerance" type="float" value="5.0"/>
+      <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_feature_mz_tolerance_unit" optional="True" type="select" value="ppm">
+        <option value="Da">Da</option>
+        <option value="ppm">ppm</option>
+      </param>
+      <param help="(-rt_tolerance) " label="Additional retention time tolerance added to feature boundaries" name="param_feature_rt_tolerance" type="float" value="0.0"/>
+      <param checked="false" falsevalue="" help="(-believe_charge) " label="Whether precursor charge is assumed correct" name="param_feature_believe_charge" optional="True" truevalue="-feature:believe_charge" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-keep_original) " label="Whether a copy of the precusor and MS2 should be made (true) or if the original should be discarded (false)" name="param_feature_keep_original" optional="True" truevalue="-feature:keep_original" type="boolean"/>
+      <param checked="false" falsevalue="" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)" label="Whether a precursor should be corrected to all matching features (true) or only the nearest (false)" name="param_feature_assign_all_matching" optional="True" truevalue="-feature:assign_all_matching" type="boolean"/>
+      <param help="(-mz_tolerance) Used to determine matching to next MS1 peak" label="The precursor mass tolerance" name="param_nearest_peak_mz_tolerance" type="float" value="0.0"/>
+      <param help="(-mz_tolerance_unit) " label="Unit of precursor mass tolerance" name="param_nearest_peak_mz_tolerance_unit" optional="True" type="select" value="ppm">
+        <option value="Da">Da</option>
+        <option value="ppm">ppm</option>
+      </param>
+      <expand macro="advanced_options">
+        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
+        <param help="(-max_trace) " label="Maximum isotopic trace considered in matching a precursor to a feature" name="param_feature_max_trace" type="integer" value="2"/>
+      </expand>
+    </inputs>
+    <outputs>
+      <data format="mzml" name="param_out"/>
+      <data format="tabular" name="param_out_csv"/>
+    </outputs>
+    <help>Corrects the precursor mass and charge determined by the instrument software.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html
-
-@REFERENCES@
-</help>
-</tool>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_HighResPrecursorMassCorrector.html</help>
+  </tool>