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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $param_algorithm_centroiding_active:
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20 -algorithm:centroiding:active
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21 #end if
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22 #if $param_algorithm_centroiding_window_width:
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23 -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
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24 #end if
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25 #if $param_algorithm_centroiding_absolute_isotope_mass_precision:
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26 -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
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27 #end if
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28 #if $param_algorithm_centroiding_relative_isotope_mass_precision:
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29 -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
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30 #end if
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31 #if $param_algorithm_centroiding_minimal_peak_height:
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32 -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
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33 #end if
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34 #if $param_algorithm_centroiding_min_ms_signal_intensity:
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35 -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
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36 #end if
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37
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38 #if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
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39 -algorithm:ms1:precursor_detection_scan_levels
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40 #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
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41 #if " " in str(token):
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42 "$token.param_algorithm_ms1_precursor_detection_scan_levels"
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43 #else
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44 $token.param_algorithm_ms1_precursor_detection_scan_levels
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45 #end if
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46 #end for
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47 #end if
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48 #if $param_algorithm_ms1_max_inter_scan_distance:
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49 -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
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50 #end if
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51 #if $param_algorithm_ms1_tr_resolution:
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52 -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
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53 #end if
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54 #if $param_algorithm_ms1_intensity_threshold:
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55 -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
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56 #end if
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57 #if $param_algorithm_ms1_max_inter_scan_rt_distance:
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58 -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
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59 #end if
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60 #if $param_algorithm_ms1_min_nb_cluster_members:
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61 -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
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62 #end if
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63 #if $param_algorithm_ms1_detectable_isotope_factor:
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64 -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
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65 #end if
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66 #if $param_algorithm_ms1_intensity_cv:
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67 -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
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68 #end if
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69 #if $param_algorithm_ms1_retention_time_tolerance:
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70 -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
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71 #end if
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72 #if $param_algorithm_ms1_mz_tolerance:
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73 -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
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74 #end if
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75 #if $param_algorithm_ms1_feature_merger_active:
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76 -algorithm:ms1_feature_merger:active
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77 #end if
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78 #if $param_algorithm_ms1_feature_merger_tr_resolution:
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79 -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
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80 #end if
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81 #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
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82 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
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83 #end if
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84 #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
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85 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
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86 #end if
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87 #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
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88 -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
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89 #end if
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90 #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
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91 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
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92 #end if
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93 #if $param_algorithm_ms1_feature_selection_options_start_elution_window:
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94 -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
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95 #end if
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96 #if $param_algorithm_ms1_feature_selection_options_end_elution_window:
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97 -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
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98 #end if
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99 #if $param_algorithm_ms1_feature_selection_options_mz_range_min:
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100 -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
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101 #end if
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102 #if $param_algorithm_ms1_feature_selection_options_mz_range_max:
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103 -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
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104 #end if
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105 #if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
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106 -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
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107 #end if
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108 #if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
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109 -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
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110 #end if
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111 #if $adv_opts.adv_opts_selector=='advanced':
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112 #if $adv_opts.param_force:
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113 -force
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114 #end if
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115 #end if
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116 </command>
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117 <inputs>
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118 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
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119 <param name="param_algorithm_centroiding_active" type="boolean" truevalue="-algorithm:centroiding:active" falsevalue="" checked="false" optional="True" label="MS1 data centroid data" help="(-active) "/>
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120 <param name="param_algorithm_centroiding_window_width" type="integer" min="1" optional="True" value="5" label="Centroid window width" help="(-window_width) "/>
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121 <param name="param_algorithm_centroiding_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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122 <param name="param_algorithm_centroiding_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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123 <param name="param_algorithm_centroiding_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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124 <param name="param_algorithm_centroiding_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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125 <repeat name="rep_param_algorithm_ms1_precursor_detection_scan_levels" min="0" max="1" title="param_algorithm_ms1_precursor_detection_scan_levels">
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126 <param name="param_algorithm_ms1_precursor_detection_scan_levels" type="text" size="30" value="1" label="Precursor detection scan levels" help="(-precursor_detection_scan_levels) ">
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127 <sanitizer>
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128 <valid initial="string.printable">
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129 <remove value="'"/>
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130 <remove value="""/>
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 </repeat>
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135 <param name="param_algorithm_ms1_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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136 <param name="param_algorithm_ms1_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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137 <param name="param_algorithm_ms1_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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138 <param name="param_algorithm_ms1_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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139 <param name="param_algorithm_ms1_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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140 <param name="param_algorithm_ms1_detectable_isotope_factor" type="float" min="0.0" optional="True" value="0.05" label="Detectable isotope facto" help="(-detectable_isotope_factor) "/>
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141 <param name="param_algorithm_ms1_intensity_cv" type="float" min="0.0" optional="True" value="0.9" label="IntensityCV" help="(-intensity_cv) "/>
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142 <param name="param_algorithm_ms1_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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143 <param name="param_algorithm_ms1_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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144 <param name="param_algorithm_ms1_feature_merger_active" type="boolean" truevalue="-algorithm:ms1_feature_merger:active" falsevalue="" checked="true" optional="True" label="Activation of MS1 feature merging post processing" help="(-active) "/>
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145 <param name="param_algorithm_ms1_feature_merger_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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146 <param name="param_algorithm_ms1_feature_merger_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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147 <param name="param_algorithm_ms1_feature_merger_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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148 <param name="param_algorithm_ms1_feature_merger_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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149 <param name="param_algorithm_ms1_feature_merger_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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150 <param name="param_algorithm_ms1_feature_selection_options_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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151 <param name="param_algorithm_ms1_feature_selection_options_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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152 <param name="param_algorithm_ms1_feature_selection_options_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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153 <param name="param_algorithm_ms1_feature_selection_options_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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154 <param name="param_algorithm_ms1_feature_selection_options_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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155 <param name="param_algorithm_ms1_feature_selection_options_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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156 <expand macro="advanced_options">
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157 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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158 </expand>
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159 </inputs>
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160 <outputs>
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161 <data name="param_out" format="featurexml"/>
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162 </outputs>
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163 <help>**What it does**
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164
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165 Finds mass spectrometric features in mass spectra.
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166
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167
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168 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html</help>
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169 <expand macro="references"/>
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170 </tool>
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