view PrecursorMassCorrector.xml @ 3:75537a09e9fa draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.0.0">
  <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

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_feature_in:
  -feature_in $param_feature_in
#end if
#if $param_precursor_mass_tolerance:
  -precursor_mass_tolerance $param_precursor_mass_tolerance
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_max_charge:
  -max_charge $adv_opts.param_max_charge
#end if
    #if $adv_opts.param_intensity_threshold:
  -intensity_threshold $adv_opts.param_intensity_threshold
#end if
    #if $adv_opts.param_force:
  -force
#end if
#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  &lt;br&gt;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; &lt;br&gt;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) "/>
      <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" 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</help>
  <expand macro="references"/>
</tool>