<?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: [Quantitation]-->
  <tool id="AdditiveSeries" name="AdditiveSeries" version="2.0.0">
    <description>Computes an additive series to quantify a peptide in a set of samples.</description>
    <macros>
      <token name="@EXECUTABLE@">AdditiveSeries</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>AdditiveSeries

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_mz_tolerance:
  -mz_tolerance $param_mz_tolerance
#end if
#if $param_rt_tolerance:
  -rt_tolerance $param_rt_tolerance
#end if

#if $rep_param_concentrations:
-concentrations
  #for token in $rep_param_concentrations:
    #if &quot; &quot; in str(token):
      &quot;$token.param_concentrations&quot;
    #else
      $token.param_concentrations
    #end if
  #end for
#end if
#if $param_feature_rt:
  -feature_rt $param_feature_rt
#end if
#if $param_feature_mz:
  -feature_mz $param_feature_mz
#end if
#if $param_standard_rt:
  -standard_rt $param_standard_rt
#end if
#if $param_standard_mz:
  -standard_mz $param_standard_mz
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_plot_write_gnuplot_output:
  -plot:write_gnuplot_output
#end if
#if $param_plot_out_gp:
  -plot:out_gp     &quot;$param_plot_out_gp&quot;
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="input files separated by blanks" 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 help="(-mz_tolerance) " label="Tolerance in m/z dimension" name="param_mz_tolerance" type="float" value="1.0"/>
      <param help="(-rt_tolerance) " label="Tolerance in RT dimension" name="param_rt_tolerance" type="float" value="1.0"/>
      <repeat min="1" name="rep_param_concentrations" title="param_concentrations">
        <param help="(-concentrations) " label="List of spiked concentrations" name="param_concentrations" size="30" type="text" value="0">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param help="(-feature_rt) " label="RT position of the feature" name="param_feature_rt" type="float" value="-1.0"/>
      <param help="(-feature_mz) " label="m/z position of the feature" name="param_feature_mz" type="float" value="-1.0"/>
      <param help="(-standard_rt) " label="RT position of the standard" name="param_standard_rt" type="float" value="-1.0"/>
      <param help="(-standard_mz) " label="m/z position of the standard" name="param_standard_mz" type="float" value="-1.0"/>
      <param checked="false" falsevalue="" help="(-write_gnuplot_output) " label="Flag that activates the GNUplot output" name="param_plot_write_gnuplot_output" optional="True" truevalue="-plot:write_gnuplot_output" type="boolean"/>
      <param help="(-out_gp) " label="base file name (3 files with different extensions are created)" name="param_plot_out_gp" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <expand macro="advanced_options">
        <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="xml" name="param_out"/>
    </outputs>
    <help>Computes an additive series to quantify a peptide in a set of samples.


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