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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="1.12.0">
  <description>Finds mass spectrometric features in mass spectra.</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FeatureFinderSuperHirn

-in ${param_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
${param_active}
-algorithm:centroiding:window_width ${param_window_width}
-algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision}
-algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision}
-algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height}
-algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity}
-algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels}
-algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance}
-algorithm:ms1:tr_resolution ${param_tr_resolution}
-algorithm:ms1:intensity_threshold ${param_intensity_threshold}
-algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance}
-algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members}
-algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor}
-algorithm:ms1:intensity_cv ${param_intensity_cv}
-algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance}
-algorithm:ms1:mz_tolerance ${param_mz_tolerance}
${param_active}
-algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution}
-algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance}
-algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance}
-algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage}
-algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering}
-algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window}
-algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window}
-algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min}
-algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max}
-algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min}
-algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/>
    <param name="param_active" type="boolean" truevalue="-algorithm:centroiding:active true" falsevalue="-algorithm:centroiding:active false" checked="false" optional="True" label="MS1 data centroid data" help="(-active)"/>
    <param name="param_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width)"/>
    <param name="param_absolute_isotope_mass_precision" type="float" min="0.0" optional="True" value="0.01" label="Absolute isotope mass precision (Da)" help="(-absolute_isotope_mass_precision)"/>
    <param name="param_relative_isotope_mass_precision" type="float" min="0.0" optional="True" value="10.0" label="Relative isotope mass precision" help="(-relative_isotope_mass_precision)"/>
    <param name="param_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height)"/>
    <param name="param_min_ms_signal_intensity" type="float" min="0.0" optional="True" value="50.0" label="Minimal Centroid MS Signal Intensity" help="(-min_ms_signal_intensity)"/>
    <param name="param_precursor_detection_scan_levels" type="text" size="20" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels)"/>
    <param name="param_max_inter_scan_distance" type="integer" min="0" optional="True" value="0" label="MS1 max inter scan distance" help="(-max_inter_scan_distance)"/>
    <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
    <param name="param_intensity_threshold" type="float" min="0.0" optional="True" value="1000.0" label="FT peak detect MS1 intensity min threshold" help="(-intensity_threshold)"/>
    <param name="param_max_inter_scan_rt_distance" type="float" min="0.0" optional="True" value="0.1" label="MS1 max inter scan distance" help="(-max_inter_scan_rt_distance)"/>
    <param name="param_min_nb_cluster_members" type="integer" min="0" optional="True" value="4" label="FT peak detect MS1 min nb peak members" help="(-min_nb_cluster_members)"/>
    <param name="param_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope factor" help="(-detectable_isotope_factor)"/>
    <param name="param_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv)"/>
    <param name="param_retention_time_tolerance" type="float" min="0.0" optional="True" value="0.5" label="MS1 retention time tolerance (minutes)" help="(-retention_time_tolerance)"/>
    <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance)"/>
    <param name="param_active" type="boolean" truevalue="-algorithm:ms1_feature_merger:active true" falsevalue="-algorithm:ms1_feature_merger:active false" checked="true" optional="True" label="Activation of MS1 feature merging post processing" help="(-active)"/>
    <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
    <param name="param_initial_apex_tr_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Initial Apex Tr tolerance" help="(-initial_apex_tr_tolerance)"/>
    <param name="param_feature_merging_tr_tolerance" type="float" min="0.0" optional="True" value="1.0" label="MS1 feature Tr merging tolerance" help="(-feature_merging_tr_tolerance)"/>
    <param name="param_intensity_variation_percentage" type="float" min="0.0" max="100.0" optional="True" value="25.0" label="Percentage of intensity variation between LC border peaks" help="(-intensity_variation_percentage)"/>
    <param name="param_ppm_tolerance_for_mz_clustering" type="float" min="0.0" optional="True" value="10.0" label="PPM value for the m/z clustering of merging candidates" help="(-ppm_tolerance_for_mz_clustering)"/>
    <param name="param_start_elution_window" type="float" min="0.0" optional="True" value="0.0" label="start elution window (minutes)" help="(-start_elution_window)"/>
    <param name="param_end_elution_window" type="float" min="0.0" optional="True" value="180.0" label="end elution window (minutes)" help="(-end_elution_window)"/>
    <param name="param_mz_range_min" type="float" min="0.0" optional="True" value="0.0" label="MS1 feature mz range min" help="(-mz_range_min)"/>
    <param name="param_mz_range_max" type="float" min="0.0" optional="True" value="2000.0" label="MS1 feature mz range max" help="(-mz_range_max)"/>
    <param name="param_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min)"/>
    <param name="param_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output peak file " format="featureXML"/>
  </outputs>
  <help>**What it does**

Finds mass spectrometric features in mass spectra.


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

@REFERENCES@
</help>
</tool>