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<?xml version='1.0' encoding='UTF-8'?>
<tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="1.12.0">
  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
  <macros>
    <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PrecursorMassCorrector

-in ${param_in}
-out ${param_out}
-feature_in ${param_feature_in}
-precursor_mass_tolerance ${param_precursor_mass_tolerance}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -max_charge ${adv_opts.param_max_charge}
    -intensity_threshold ${adv_opts.param_intensity_threshold}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="Input mzML file containing the spectra." help="(-in)"/>
    <param name="param_feature_in" type="data" format="featureXML" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries #br#will be matched to the feature m/z values if possible." help="(-feature_in)"/>
    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected;#br#this value should be set to the instruments selection window." help="(-precursor_mass_tolerance)"/>
    <expand macro="advanced_options">
      <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge)"/>
      <param name="param_intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details." help="(-intensity_threshold)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output mzML file." format="mzML"/>
  </outputs>
  <help>**What it does**

Corrects the precursor entries of MS/MS spectra, by using MS1 information.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html

@REFERENCES@
</help>
</tool>