<?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="FeatureFinderMRM" name="FeatureFinderMRM" version="2.0.0">
    <description>Detects two-dimensional features in LC-MS data.</description>
    <macros>
      <token name="@EXECUTABLE@">FeatureFinderMRM</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>FeatureFinderMRM

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
-threads \${GALAXY_SLOTS:-24}
#if $param_algorithm_min_rt_distance:
  -algorithm:min_rt_distance $param_algorithm_min_rt_distance
#end if
#if $param_algorithm_min_signal_to_noise_ratio:
  -algorithm:min_signal_to_noise_ratio $param_algorithm_min_signal_to_noise_ratio
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_min_num_peaks_per_feature:
  -algorithm:min_num_peaks_per_feature $adv_opts.param_algorithm_min_num_peaks_per_feature
#end if
    #if $adv_opts.param_algorithm_write_debug_files:
  -algorithm:write_debug_files
#end if
    #if $adv_opts.param_algorithm_resample_traces:
  -algorithm:resample_traces
#end if
    #if $adv_opts.param_algorithm_write_debuginfo:
  -algorithm:write_debuginfo
#end if
#end if
</command>
    <inputs>
      <param format="mzml" help="(-in) " label="input file" name="param_in" optional="False" type="data"/>
      <param help="(-min_rt_distance) " label="Minimal distance of MRM features in seconds" min="0.0" name="param_algorithm_min_rt_distance" optional="True" type="float" value="10.0"/>
      <param help="(-min_signal_to_noise_ratio) Set to zero if the MRM-traces contains mostly signals, and no noise" label="Minimal S/N ratio a peak must have to be taken into account" min="0.0" name="param_algorithm_min_signal_to_noise_ratio" optional="True" type="float" value="2.0"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-min_num_peaks_per_feature) " label="Minimal number of peaks which are needed for a single feature" min="1" name="param_algorithm_min_num_peaks_per_feature" optional="True" type="integer" value="5"/>
        <param checked="false" falsevalue="" help="(-write_debug_files) " label="If set to true, for each feature a plot will be created, in the subdirectory 'debug'" name="param_algorithm_write_debug_files" optional="True" truevalue="-algorithm:write_debug_files" type="boolean"/>
        <param checked="false" falsevalue="" help="(-resample_traces) " label="If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension" name="param_algorithm_resample_traces" optional="True" truevalue="-algorithm:resample_traces" type="boolean"/>
        <param checked="false" falsevalue="" help="(-write_debuginfo) " label="If set to true, debug messages are written, the output can be somewhat lengthy" name="param_algorithm_write_debuginfo" optional="True" truevalue="-algorithm:write_debuginfo" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
    </outputs>
    <help>Detects two-dimensional features in LC-MS data.


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