<?xml version='1.0' encoding='UTF-8'?>
<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="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 $param_type:
  -type
  #if " " in str($param_type):
    "$param_type"
  #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 $param_algorithm_mz_tolerance_unit:
  -algorithm:mz_tolerance_unit
  #if " " in str($param_algorithm_mz_tolerance_unit):
    "$param_algorithm_mz_tolerance_unit"
  #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 name="param_in" type="data" format="featurexml,mzml" optional="False" label="input peak file" help="(-in) "/>
    <param name="param_ref_peaks" type="data" format="tabular,idxml" optional="True" label="input file containing reference m/z values (either as textfile with one m/z per line and no header or as idXML file)" help="(-ref_peaks) "/>
    <param name="param_type" type="select" optional="True" value="spectrumwise" label="The kind of internal calibration that should be applied" help="(-type) ">
      <option value="spectrumwise">spectrumwise</option>
      <option value="global">global</option>
    </param>
    <param name="param_algorithm_mz_tolerance" type="float" min="0.0" optional="True" value="1.0" label="Allowed tolerance between peak and reference m/z" help="(-mz_tolerance) "/>
    <param name="param_algorithm_mz_tolerance_unit" type="select" optional="True" value="Da" label="Unit for mz_tolerance" help="(-mz_tolerance_unit) ">
      <option value="Da">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <param name="param_algorithm_rt_tolerance" type="integer" value="10" label="Allowed tolerance between peak and reference rt" help="(-rt_tolerance) "/>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" metadata_source="param_in" format="input"/>
    <data name="param_trafo" format="trafoxml"/>
  </outputs>
  <help>**What it does**

Applies an internal calibration.


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