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annotate FeatureFinderSuperHirn.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderSuperHirn" name="FeatureFinderSuperHirn" version="2.0.0">
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5 <description>Finds mass spectrometric features in mass spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderSuperHirn</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FeatureFinderSuperHirn
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 -threads \${GALAXY_SLOTS:-24}
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22 #if $param_algorithm_centroiding_active:
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23 -algorithm:centroiding:active
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24 #end if
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25 #if $param_algorithm_centroiding_window_width:
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26 -algorithm:centroiding:window_width $param_algorithm_centroiding_window_width
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27 #end if
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28 #if $param_algorithm_centroiding_absolute_isotope_mass_precision:
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29 -algorithm:centroiding:absolute_isotope_mass_precision $param_algorithm_centroiding_absolute_isotope_mass_precision
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30 #end if
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31 #if $param_algorithm_centroiding_relative_isotope_mass_precision:
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32 -algorithm:centroiding:relative_isotope_mass_precision $param_algorithm_centroiding_relative_isotope_mass_precision
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33 #end if
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34 #if $param_algorithm_centroiding_minimal_peak_height:
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35 -algorithm:centroiding:minimal_peak_height $param_algorithm_centroiding_minimal_peak_height
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36 #end if
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37 #if $param_algorithm_centroiding_min_ms_signal_intensity:
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38 -algorithm:centroiding:min_ms_signal_intensity $param_algorithm_centroiding_min_ms_signal_intensity
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39 #end if
0
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40
4
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41 #if $rep_param_algorithm_ms1_precursor_detection_scan_levels:
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42 -algorithm:ms1:precursor_detection_scan_levels
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43 #for token in $rep_param_algorithm_ms1_precursor_detection_scan_levels:
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44 #if &quot; &quot; in str(token):
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45 &quot;$token.param_algorithm_ms1_precursor_detection_scan_levels&quot;
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46 #else
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47 $token.param_algorithm_ms1_precursor_detection_scan_levels
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48 #end if
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49 #end for
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50 #end if
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51 #if $param_algorithm_ms1_max_inter_scan_distance:
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52 -algorithm:ms1:max_inter_scan_distance $param_algorithm_ms1_max_inter_scan_distance
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53 #end if
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54 #if $param_algorithm_ms1_tr_resolution:
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55 -algorithm:ms1:tr_resolution $param_algorithm_ms1_tr_resolution
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56 #end if
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57 #if $param_algorithm_ms1_intensity_threshold:
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58 -algorithm:ms1:intensity_threshold $param_algorithm_ms1_intensity_threshold
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59 #end if
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60 #if $param_algorithm_ms1_max_inter_scan_rt_distance:
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61 -algorithm:ms1:max_inter_scan_rt_distance $param_algorithm_ms1_max_inter_scan_rt_distance
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62 #end if
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63 #if $param_algorithm_ms1_min_nb_cluster_members:
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64 -algorithm:ms1:min_nb_cluster_members $param_algorithm_ms1_min_nb_cluster_members
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65 #end if
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66 #if $param_algorithm_ms1_detectable_isotope_factor:
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67 -algorithm:ms1:detectable_isotope_factor $param_algorithm_ms1_detectable_isotope_factor
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68 #end if
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69 #if $param_algorithm_ms1_intensity_cv:
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70 -algorithm:ms1:intensity_cv $param_algorithm_ms1_intensity_cv
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71 #end if
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72 #if $param_algorithm_ms1_retention_time_tolerance:
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73 -algorithm:ms1:retention_time_tolerance $param_algorithm_ms1_retention_time_tolerance
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74 #end if
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75 #if $param_algorithm_ms1_mz_tolerance:
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76 -algorithm:ms1:mz_tolerance $param_algorithm_ms1_mz_tolerance
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77 #end if
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78 #if $param_algorithm_ms1_feature_merger_active:
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79 -algorithm:ms1_feature_merger:active
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80 #end if
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81 #if $param_algorithm_ms1_feature_merger_tr_resolution:
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82 -algorithm:ms1_feature_merger:tr_resolution $param_algorithm_ms1_feature_merger_tr_resolution
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83 #end if
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84 #if $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance:
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85 -algorithm:ms1_feature_merger:initial_apex_tr_tolerance $param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance
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86 #end if
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87 #if $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance:
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88 -algorithm:ms1_feature_merger:feature_merging_tr_tolerance $param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance
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89 #end if
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90 #if $param_algorithm_ms1_feature_merger_intensity_variation_percentage:
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91 -algorithm:ms1_feature_merger:intensity_variation_percentage $param_algorithm_ms1_feature_merger_intensity_variation_percentage
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92 #end if
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93 #if $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering:
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94 -algorithm:ms1_feature_merger:ppm_tolerance_for_mz_clustering $param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering
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95 #end if
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96 #if $param_algorithm_ms1_feature_selection_options_start_elution_window:
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97 -algorithm:ms1_feature_selection_options:start_elution_window $param_algorithm_ms1_feature_selection_options_start_elution_window
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98 #end if
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99 #if $param_algorithm_ms1_feature_selection_options_end_elution_window:
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100 -algorithm:ms1_feature_selection_options:end_elution_window $param_algorithm_ms1_feature_selection_options_end_elution_window
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101 #end if
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102 #if $param_algorithm_ms1_feature_selection_options_mz_range_min:
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103 -algorithm:ms1_feature_selection_options:mz_range_min $param_algorithm_ms1_feature_selection_options_mz_range_min
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104 #end if
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105 #if $param_algorithm_ms1_feature_selection_options_mz_range_max:
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106 -algorithm:ms1_feature_selection_options:mz_range_max $param_algorithm_ms1_feature_selection_options_mz_range_max
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107 #end if
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108 #if $param_algorithm_ms1_feature_selection_options_chrg_range_min:
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109 -algorithm:ms1_feature_selection_options:chrg_range_min $param_algorithm_ms1_feature_selection_options_chrg_range_min
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110 #end if
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111 #if $param_algorithm_ms1_feature_selection_options_chrg_range_max:
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112 -algorithm:ms1_feature_selection_options:chrg_range_max $param_algorithm_ms1_feature_selection_options_chrg_range_max
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113 #end if
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114 #if $adv_opts.adv_opts_selector=='advanced':
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115 #if $adv_opts.param_force:
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116 -force
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117 #end if
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118 #end if
0
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119 </command>
4
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120 <inputs>
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121 <param format="mzml" help="(-in) " label="input profile data file" name="param_in" optional="False" type="data"/>
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122 <param checked="false" falsevalue="" help="(-active) " label="MS1 data centroid data" name="param_algorithm_centroiding_active" optional="True" truevalue="-algorithm:centroiding:active" type="boolean"/>
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123 <param help="(-window_width) " label="Centroid window width" min="1" name="param_algorithm_centroiding_window_width" optional="True" type="integer" value="5"/>
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124 <param help="(-absolute_isotope_mass_precision) " label="Absolute isotope mass precision (Da)" min="0.0" name="param_algorithm_centroiding_absolute_isotope_mass_precision" optional="True" type="float" value="0.01"/>
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125 <param help="(-relative_isotope_mass_precision) " label="Relative isotope mass precision" min="0.0" name="param_algorithm_centroiding_relative_isotope_mass_precision" optional="True" type="float" value="10.0"/>
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126 <param help="(-minimal_peak_height) " label="Minimal peak height" min="0.0" name="param_algorithm_centroiding_minimal_peak_height" optional="True" type="float" value="0.0"/>
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127 <param help="(-min_ms_signal_intensity) " label="Minimal Centroid MS Signal Intensity" min="0.0" name="param_algorithm_centroiding_min_ms_signal_intensity" optional="True" type="float" value="50.0"/>
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128 <repeat max="1" min="0" name="rep_param_algorithm_ms1_precursor_detection_scan_levels" title="param_algorithm_ms1_precursor_detection_scan_levels">
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129 <param help="(-precursor_detection_scan_levels) " label="Precursor detection scan levels" name="param_algorithm_ms1_precursor_detection_scan_levels" size="30" type="text" value="1">
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130 <sanitizer>
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131 <valid initial="string.printable">
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132 <remove value="'"/>
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133 <remove value="&quot;"/>
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134 </valid>
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135 </sanitizer>
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136 </param>
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137 </repeat>
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138 <param help="(-max_inter_scan_distance) " label="MS1 max inter scan distance" min="0" name="param_algorithm_ms1_max_inter_scan_distance" optional="True" type="integer" value="0"/>
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139 <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_tr_resolution" optional="True" type="float" value="0.01"/>
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140 <param help="(-intensity_threshold) " label="FT peak detect MS1 intensity min threshold" min="0.0" name="param_algorithm_ms1_intensity_threshold" optional="True" type="float" value="1000.0"/>
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141 <param help="(-max_inter_scan_rt_distance) " label="MS1 max inter scan distance" min="0.0" name="param_algorithm_ms1_max_inter_scan_rt_distance" optional="True" type="float" value="0.1"/>
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142 <param help="(-min_nb_cluster_members) " label="FT peak detect MS1 min nb peak members" min="0" name="param_algorithm_ms1_min_nb_cluster_members" optional="True" type="integer" value="4"/>
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143 <param help="(-detectable_isotope_factor) " label="Detectable isotope facto" min="0.0" name="param_algorithm_ms1_detectable_isotope_factor" optional="True" type="float" value="0.05"/>
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144 <param help="(-intensity_cv) " label="IntensityCV" min="0.0" name="param_algorithm_ms1_intensity_cv" optional="True" type="float" value="0.9"/>
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145 <param help="(-retention_time_tolerance) " label="MS1 retention time tolerance (minutes)" min="0.0" name="param_algorithm_ms1_retention_time_tolerance" optional="True" type="float" value="0.5"/>
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146 <param help="(-mz_tolerance) " label="MS1 m/z tolerance (ppm)" min="0.0" name="param_algorithm_ms1_mz_tolerance" optional="True" type="float" value="0.0"/>
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147 <param checked="true" falsevalue="" help="(-active) " label="Activation of MS1 feature merging post processing" name="param_algorithm_ms1_feature_merger_active" optional="True" truevalue="-algorithm:ms1_feature_merger:active" type="boolean"/>
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148 <param help="(-tr_resolution) " label="MS1 LC retention time resolution" min="0.0" name="param_algorithm_ms1_feature_merger_tr_resolution" optional="True" type="float" value="0.01"/>
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149 <param help="(-initial_apex_tr_tolerance) " label="Initial Apex Tr tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_initial_apex_tr_tolerance" optional="True" type="float" value="5.0"/>
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150 <param help="(-feature_merging_tr_tolerance) " label="MS1 feature Tr merging tolerance" min="0.0" name="param_algorithm_ms1_feature_merger_feature_merging_tr_tolerance" optional="True" type="float" value="1.0"/>
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151 <param help="(-intensity_variation_percentage) " label="Percentage of intensity variation between LC border peaks" max="100.0" min="0.0" name="param_algorithm_ms1_feature_merger_intensity_variation_percentage" optional="True" type="float" value="25.0"/>
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152 <param help="(-ppm_tolerance_for_mz_clustering) " label="PPM value for the m/z clustering of merging candidates" min="0.0" name="param_algorithm_ms1_feature_merger_ppm_tolerance_for_mz_clustering" optional="True" type="float" value="10.0"/>
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153 <param help="(-start_elution_window) " label="start elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_start_elution_window" optional="True" type="float" value="0.0"/>
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154 <param help="(-end_elution_window) " label="end elution window (minutes)" min="0.0" name="param_algorithm_ms1_feature_selection_options_end_elution_window" optional="True" type="float" value="180.0"/>
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155 <param help="(-mz_range_min) " label="MS1 feature mz range min" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_min" optional="True" type="float" value="0.0"/>
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156 <param help="(-mz_range_max) " label="MS1 feature mz range max" min="0.0" name="param_algorithm_ms1_feature_selection_options_mz_range_max" optional="True" type="float" value="2000.0"/>
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157 <param help="(-chrg_range_min) " label="MS1 feature CHRG range min" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_min" optional="True" type="integer" value="1"/>
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158 <param help="(-chrg_range_max) " label="MS1 feature CHRG range max" min="0" name="param_algorithm_ms1_feature_selection_options_chrg_range_max" optional="True" type="integer" value="5"/>
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159 <expand macro="advanced_options">
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160 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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161 </expand>
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162 </inputs>
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163 <outputs>
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164 <data format="xml" name="param_out"/>
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165 </outputs>
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166 <help>Finds mass spectrometric features in mass spectra.
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167
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168
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169 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderSuperHirn.html</help>
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170 </tool>