<?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

#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 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</help>
  </tool>