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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="1.12.0">
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3 <description>Finds mass spectrometric features in mass spectra.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FeatureFinderSuperHirn
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11
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12 -in ${param_in}
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13 -out ${param_out}
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14 -threads \${GALAXY_SLOTS:-24}
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15 ${param_active}
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16 -algorithm:centroiding:window_width ${param_window_width}
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17 -algorithm:centroiding:absolute_isotope_mass_precision ${param_absolute_isotope_mass_precision}
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18 -algorithm:centroiding:relative_isotope_mass_precision ${param_relative_isotope_mass_precision}
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19 -algorithm:centroiding:minimal_peak_height ${param_minimal_peak_height}
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20 -algorithm:centroiding:min_ms_signal_intensity ${param_min_ms_signal_intensity}
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21 -algorithm:ms1:precursor_detection_scan_levels ${param_precursor_detection_scan_levels}
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22 -algorithm:ms1:max_inter_scan_distance ${param_max_inter_scan_distance}
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23 -algorithm:ms1:tr_resolution ${param_tr_resolution}
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24 -algorithm:ms1:intensity_threshold ${param_intensity_threshold}
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25 -algorithm:ms1:max_inter_scan_rt_distance ${param_max_inter_scan_rt_distance}
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26 -algorithm:ms1:min_nb_cluster_members ${param_min_nb_cluster_members}
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27 -algorithm:ms1:detectable_isotope_factor ${param_detectable_isotope_factor}
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28 -algorithm:ms1:intensity_cv ${param_intensity_cv}
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29 -algorithm:ms1:retention_time_tolerance ${param_retention_time_tolerance}
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30 -algorithm:ms1:mz_tolerance ${param_mz_tolerance}
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31 ${param_active}
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32 -algorithm:ms1_feature_merger:tr_resolution ${param_tr_resolution}
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33 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance ${param_initial_apex_tr_tolerance}
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34 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance ${param_feature_merging_tr_tolerance}
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35 -algorithm:ms1_feature_merger:intensity_variation_percentage ${param_intensity_variation_percentage}
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36 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering ${param_ppm_tolerance_for_mz_clustering}
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37 -algorithm:ms1_feature_selection_options:start_elution_window ${param_start_elution_window}
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38 -algorithm:ms1_feature_selection_options:end_elution_window ${param_end_elution_window}
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39 -algorithm:ms1_feature_selection_options:mz_range_min ${param_mz_range_min}
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40 -algorithm:ms1_feature_selection_options:mz_range_max ${param_mz_range_max}
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41 -algorithm:ms1_feature_selection_options:chrg_range_min ${param_chrg_range_min}
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42 -algorithm:ms1_feature_selection_options:chrg_range_max ${param_chrg_range_max}
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43 </command>
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44 <inputs>
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45 <param name="param_in" type="data" format="mzML" optional="False" label="input profile data file " help="(-in)"/>
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46 <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)"/>
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47 <param name="param_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width)"/>
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48 <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)"/>
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49 <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)"/>
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50 <param name="param_minimal_peak_height" type="float" min="0.0" optional="True" value="0.0" label="Minimal peak height" help="(-minimal_peak_height)"/>
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51 <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)"/>
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52 <param name="param_precursor_detection_scan_levels" type="text" size="20" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels)"/>
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53 <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)"/>
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54 <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
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55 <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)"/>
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56 <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)"/>
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57 <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)"/>
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58 <param name="param_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope factor" help="(-detectable_isotope_factor)"/>
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59 <param name="param_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv)"/>
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60 <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)"/>
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61 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="0.0" label="MS1 m/z tolerance (ppm)" help="(-mz_tolerance)"/>
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62 <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)"/>
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63 <param name="param_tr_resolution" type="float" min="0.0" optional="True" value="0.01" label="MS1 LC retention time resolution" help="(-tr_resolution)"/>
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64 <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)"/>
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65 <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)"/>
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66 <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)"/>
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67 <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)"/>
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68 <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)"/>
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69 <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)"/>
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70 <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)"/>
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71 <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)"/>
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72 <param name="param_chrg_range_min" type="integer" min="0" optional="True" value="1" label="MS1 feature CHRG range min" help="(-chrg_range_min)"/>
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73 <param name="param_chrg_range_max" type="integer" min="0" optional="True" value="5" label="MS1 feature CHRG range max" help="(-chrg_range_max)"/>
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74 </inputs>
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75 <outputs>
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76 <data name="param_out" label="output peak file " format="featureXML"/>
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77 </outputs>
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78 <help>**What it does**
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79
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80 Finds mass spectrometric features in mass spectra.
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81
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82
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83 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html
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84
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85 @REFERENCES@
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86 </help>
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87 </tool>
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