view MetaboliteSpectralMatcher.xml @ 3:ec62782f6c68 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MetaboliteSpectralMatcher" name="MetaboliteSpectralMatcher" version="1.12.0">
  <description>Find potential HMDB ids within the given mass error window.</description>
  <macros>
    <token name="@EXECUTABLE@">MetaboliteSpectralMatcher</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MetaboliteSpectralMatcher

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:prec_mass_error_value ${param_prec_mass_error_value}
-algorithm:frag_mass_error_value ${param_frag_mass_error_value}
-algorithm:mass_error_unit ${param_mass_error_unit}
-algorithm:report_mode ${param_report_mode}
-algorithm:ionization_mode ${param_ionization_mode}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="mzML file" help="(-in)"/>
    <param name="param_prec_mass_error_value" type="float" value="100.0" label="Error allowed for precursor ion mass." help="(-prec_mass_error_value)"/>
    <param name="param_frag_mass_error_value" type="float" value="500.0" label="Error allowed for product ions." help="(-frag_mass_error_value)"/>
    <param name="param_mass_error_unit" type="select" optional="True" value="ppm" label="Unit of mass error (ppm or Da)" help="(-mass_error_unit)">
      <option value="ppm">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="param_report_mode" type="select" optional="True" value="top3" label="Which results shall be reported: the top-three scoring ones or the best scoring one?" help="(-report_mode)">
      <option value="top3">top3</option>
      <option value="best">best</option>
    </param>
    <param name="param_ionization_mode" type="select" optional="True" value="positive" label="Positive or negative ionization mode?" help="(-ionization_mode)">
      <option value="positive">positive</option>
      <option value="negative">negative</option>
    </param>
  </inputs>
  <outputs>
    <data name="param_out" label="mzTab file" format="tabular"/>
  </outputs>
  <help>**What it does**

Find potential HMDB ids within the given mass error window.


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

@REFERENCES@
</help>
</tool>