<?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="InternalCalibration" name="InternalCalibration" version="2.0.0">
    <description>Applies an internal calibration.</description>
    <macros>
      <token name="@EXECUTABLE@">InternalCalibration</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>InternalCalibration

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_ref_peaks:
  -ref_peaks $param_ref_peaks
#end if
#if $param_type:
  -type
  #if &quot; &quot; in str($param_type):
    &quot;$param_type&quot;
  #else
    $param_type
  #end if
#end if
#if $param_trafo:
  -trafo $param_trafo
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_mz_tolerance:
  -algorithm:mz_tolerance $param_algorithm_mz_tolerance
#end if
#if $param_algorithm_mz_tolerance_unit:
  -algorithm:mz_tolerance_unit
  #if &quot; &quot; in str($param_algorithm_mz_tolerance_unit):
    &quot;$param_algorithm_mz_tolerance_unit&quot;
  #else
    $param_algorithm_mz_tolerance_unit
  #end if
#end if
#if $param_algorithm_rt_tolerance:
  -algorithm:rt_tolerance $param_algorithm_rt_tolerance
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml,mzml" help="(-in) " label="input peak file" name="param_in" optional="False" type="data"/>
      <param format="tabular,xml" help="(-ref_peaks) " label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" name="param_ref_peaks" optional="True" type="data"/>
      <param help="(-type) " label="The kind of internal calibration that should be applied" name="param_type" optional="True" type="select" value="spectrumwise">
        <option value="spectrumwise">spectrumwise</option>
        <option value="global">global</option>
      </param>
      <param help="(-mz_tolerance) " label="Allowed tolerance between peak and reference m/z" min="0.0" name="param_algorithm_mz_tolerance" optional="True" type="float" value="1.0"/>
      <param help="(-mz_tolerance_unit) " label="Unit for mz_tolerance" name="param_algorithm_mz_tolerance_unit" optional="True" type="select" value="Da">
        <option value="Da">Da</option>
        <option value="ppm">ppm</option>
      </param>
      <param help="(-rt_tolerance) " label="Allowed tolerance between peak and reference rt" name="param_algorithm_rt_tolerance" type="integer" value="10"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="input" metadata_source="param_in" name="param_out"/>
      <data format="trafoxml" name="param_trafo"/>
    </outputs>
    <help>Applies an internal calibration.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InternalCalibration.html</help>
  </tool>