--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/HighResPrecursorMassCorrector.xml	Wed Mar 01 12:55:06 2017 -0500
@@ -0,0 +1,90 @@
+<?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="2.1.0">
+  <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
+
+#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
+#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 $param_feature_mz_tolerance_unit
+#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 $param_nearest_peak_mz_tolerance_unit
+#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) "/>
+    <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Features used to correct precursor masses" help="(-in) "/>
+    <param name="param_feature_mz_tolerance" type="float" value="5.0" label="The precursor mass tolerance" help="(-mz_tolerance) Used to determine matching to feature mass traces"/>
+    <param name="param_feature_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
+      <option value="Da">Da</option>
+      <option value="ppm" selected="true">ppm</option>
+    </param>
+    <param name="param_feature_rt_tolerance" type="float" value="0.0" label="Additional retention time tolerance added to feature boundaries" help="(-rt_tolerance) "/>
+    <param name="param_feature_believe_charge" display="radio" type="boolean" truevalue="-feature:believe_charge" falsevalue="" checked="false" optional="True" label="Assume precursor charge to be correct" help="(-believe_charge) "/>
+    <param name="param_feature_keep_original" display="radio" type="boolean" truevalue="-feature:keep_original" falsevalue="" checked="false" optional="True" label="Make a copy of the precursor and MS2 (true) or discard the original (false)" help="(-keep_original) "/>
+    <param name="param_feature_assign_all_matching" display="radio" type="boolean" truevalue="-feature:assign_all_matching" falsevalue="" checked="false" optional="True" label="Correct a precursor using all matching features (true) or only the nearest (false)" help="(-assign_all_matching) Only evaluated if copies are created (feature:keep_original)"/>
+    <param name="param_nearest_peak_mz_tolerance" type="float" value="0.0" label="The precursor mass tolerance to find the closest MS1 peak" help="(-mz_tolerance) Set to 0.0 to disable"/>
+    <param name="param_nearest_peak_mz_tolerance_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance" help="(-mz_tolerance_unit) ">
+      <option value="Da">Da</option>
+      <option value="ppm" selected="true">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_feature_max_trace" type="integer" value="2" label="Maximum isotopic trace considered in matching a precursor to a feature" help="(-max_trace) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzml"/>
+    <data name="param_out_csv" format="tabular"/>
+  </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</help>
+</tool>