<?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: [Utilities]-->
  <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.0.0">
    <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
    <macros>
      <token name="@EXECUTABLE@">IDMassAccuracy</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>IDMassAccuracy

-in
  #for token in $param_in:
    $token
  #end for
-id_in
  #for token in $param_id_in:
    $token
  #end for
#if $param_precursor_out:
  -precursor_out $param_precursor_out
#end if

#if $rep_param_precursor_columns:
-precursor_columns
  #for token in $rep_param_precursor_columns:
    #if &quot; &quot; in str(token):
      &quot;$token.param_precursor_columns&quot;
    #else
      $token.param_precursor_columns
    #end if
  #end for
#end if
#if $param_precursor_error_ppm:
  -precursor_error_ppm
#end if
#if $param_fragment_out:
  -fragment_out $param_fragment_out
#end if

#if $rep_param_fragment_columns:
-fragment_columns
  #for token in $rep_param_fragment_columns:
    #if &quot; &quot; in str(token):
      &quot;$token.param_fragment_columns&quot;
    #else
      $token.param_fragment_columns
    #end if
  #end for
#end if
#if $param_fragment_error_ppm:
  -fragment_error_ppm
#end if
#if $param_fragment_mass_tolerance:
  -fragment_mass_tolerance $param_fragment_mass_tolerance
#end if
#if $param_separator:
  -separator     &quot;$param_separator&quot;
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_number_of_bins:
  -number_of_bins $adv_opts.param_number_of_bins
#end if
    #if $adv_opts.param_generate_gnuplot_scripts:
  -generate_gnuplot_scripts
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="Input mzML file list, containing the spectra" multiple="true" name="param_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param format="xml" help="(-id_in) " label="Input idXML file list, containing the identifications" multiple="true" name="param_id_in" optional="False" size="30" type="data">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <repeat max="1" min="0" name="rep_param_precursor_columns" title="param_precursor_columns">
        <param help="(-precursor_columns) " label="Columns which will be written to the output file" name="param_precursor_columns" size="30" type="text" value="MassDifference">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param checked="false" falsevalue="" help="(-precursor_error_ppm) " label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" name="param_precursor_error_ppm" optional="True" truevalue="-precursor_error_ppm" type="boolean"/>
      <repeat max="1" min="0" name="rep_param_fragment_columns" title="param_fragment_columns">
        <param help="(-fragment_columns) " label="Columns which will be written to the output file" name="param_fragment_columns" size="30" type="text" value="MassDifference">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param checked="false" falsevalue="" help="(-fragment_error_ppm) " label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" name="param_fragment_error_ppm" optional="True" truevalue="-fragment_error_ppm" type="boolean"/>
      <param help="(-fragment_mass_tolerance) " label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" name="param_fragment_mass_tolerance" type="float" value="0.5"/>
      <param help="(-separator) " label="character which should be used to separate the columns in the output files" name="param_separator" size="30" type="text" value=" ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <expand macro="advanced_options">
        <param help="(-number_of_bins) " label="Number of bins that should be used to calculate the histograms for the fitting" min="10" name="param_number_of_bins" optional="True" type="integer" value="100"/>
        <param checked="false" falsevalue="" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" name="param_generate_gnuplot_scripts" optional="True" truevalue="-generate_gnuplot_scripts" type="boolean"/>
        <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="tabular" name="param_precursor_out"/>
      <data format="tabular" name="param_fragment_out"/>
    </outputs>
    <help>Calculates a distribution of the mass error from given mass spectra and IDs.


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