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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FeatureFinderCentroided" name="FeatureFinderCentroided" version="2.0.0">
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3 <description>Detects two-dimensional features in LC-MS data.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FeatureFinderCentroided</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>FeatureFinderCentroided
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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 #if $param_seeds:
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19 -seeds $param_seeds
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20 #end if
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21 #if $param_out_mzq:
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22 -out_mzq $param_out_mzq
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23 #end if
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24 -threads \${GALAXY_SLOTS:-24}
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25 #if $param_algorithm_intensity_bins:
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26 -algorithm:intensity:bins $param_algorithm_intensity_bins
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27 #end if
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28 #if $param_algorithm_mass_trace_mz_tolerance:
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29 -algorithm:mass_trace:mz_tolerance $param_algorithm_mass_trace_mz_tolerance
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30 #end if
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31 #if $param_algorithm_mass_trace_min_spectra:
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32 -algorithm:mass_trace:min_spectra $param_algorithm_mass_trace_min_spectra
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33 #end if
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34 #if $param_algorithm_mass_trace_max_missing:
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35 -algorithm:mass_trace:max_missing $param_algorithm_mass_trace_max_missing
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36 #end if
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37 #if $param_algorithm_mass_trace_slope_bound:
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38 -algorithm:mass_trace:slope_bound $param_algorithm_mass_trace_slope_bound
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39 #end if
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40 #if $param_algorithm_isotopic_pattern_charge_low:
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41 -algorithm:isotopic_pattern:charge_low $param_algorithm_isotopic_pattern_charge_low
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42 #end if
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43 #if $param_algorithm_isotopic_pattern_charge_high:
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44 -algorithm:isotopic_pattern:charge_high $param_algorithm_isotopic_pattern_charge_high
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45 #end if
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46 #if $param_algorithm_isotopic_pattern_mz_tolerance:
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47 -algorithm:isotopic_pattern:mz_tolerance $param_algorithm_isotopic_pattern_mz_tolerance
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48 #end if
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49 #if $param_algorithm_seed_min_score:
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50 -algorithm:seed:min_score $param_algorithm_seed_min_score
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51 #end if
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52 #if $param_algorithm_feature_min_score:
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53 -algorithm:feature:min_score $param_algorithm_feature_min_score
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54 #end if
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55 #if $param_algorithm_feature_reported_mz:
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56 -algorithm:feature:reported_mz
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57 #if " " in str($param_algorithm_feature_reported_mz):
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58 "$param_algorithm_feature_reported_mz"
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59 #else
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60 $param_algorithm_feature_reported_mz
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61 #end if
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62 #end if
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63 #if $param_algorithm_user_seed_rt_tolerance:
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64 -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
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65 #end if
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66 #if $param_algorithm_user_seed_mz_tolerance:
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67 -algorithm:user-seed:mz_tolerance $param_algorithm_user_seed_mz_tolerance
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68 #end if
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69 #if $param_algorithm_user_seed_min_score:
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70 -algorithm:user-seed:min_score $param_algorithm_user_seed_min_score
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71 #end if
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72 #if $adv_opts.adv_opts_selector=='advanced':
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73 #if $adv_opts.param_force:
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74 -force
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75 #end if
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76 #if $adv_opts.param_algorithm_debug_pseudo_rt_shift:
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77 -algorithm:debug:pseudo_rt_shift $adv_opts.param_algorithm_debug_pseudo_rt_shift
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78 #end if
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79 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage:
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80 -algorithm:isotopic_pattern:intensity_percentage $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage
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81 #end if
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82 #if $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional:
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83 -algorithm:isotopic_pattern:intensity_percentage_optional $adv_opts.param_algorithm_isotopic_pattern_intensity_percentage_optional
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84 #end if
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85 #if $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement:
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86 -algorithm:isotopic_pattern:optional_fit_improvement $adv_opts.param_algorithm_isotopic_pattern_optional_fit_improvement
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87 #end if
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88 #if $adv_opts.param_algorithm_isotopic_pattern_mass_window_width:
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89 -algorithm:isotopic_pattern:mass_window_width $adv_opts.param_algorithm_isotopic_pattern_mass_window_width
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90 #end if
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91 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_12C:
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92 -algorithm:isotopic_pattern:abundance_12C $adv_opts.param_algorithm_isotopic_pattern_abundance_12C
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93 #end if
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94 #if $adv_opts.param_algorithm_isotopic_pattern_abundance_14N:
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95 -algorithm:isotopic_pattern:abundance_14N $adv_opts.param_algorithm_isotopic_pattern_abundance_14N
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96 #end if
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97 #if $adv_opts.param_algorithm_fit_max_iterations:
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98 -algorithm:fit:max_iterations $adv_opts.param_algorithm_fit_max_iterations
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99 #end if
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100 #if $adv_opts.param_algorithm_feature_min_isotope_fit:
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101 -algorithm:feature:min_isotope_fit $adv_opts.param_algorithm_feature_min_isotope_fit
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102 #end if
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103 #if $adv_opts.param_algorithm_feature_min_trace_score:
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104 -algorithm:feature:min_trace_score $adv_opts.param_algorithm_feature_min_trace_score
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105 #end if
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106 #if $adv_opts.param_algorithm_feature_min_rt_span:
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107 -algorithm:feature:min_rt_span $adv_opts.param_algorithm_feature_min_rt_span
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108 #end if
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109 #if $adv_opts.param_algorithm_feature_max_rt_span:
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110 -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
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111 #end if
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112 #if $adv_opts.param_algorithm_feature_rt_shape:
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113 -algorithm:feature:rt_shape
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114 #if " " in str($adv_opts.param_algorithm_feature_rt_shape):
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115 "$adv_opts.param_algorithm_feature_rt_shape"
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116 #else
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117 $adv_opts.param_algorithm_feature_rt_shape
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118 #end if
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119 #end if
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120 #if $adv_opts.param_algorithm_feature_max_intersection:
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121 -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
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122 #end if
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123 #end if
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124 </command>
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125 <inputs>
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126 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/>
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127 <param name="param_seeds" type="data" format="featurexml" optional="True" label="User specified seed list" help="(-seeds) "/>
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128 <param name="param_algorithm_intensity_bins" type="integer" min="1" optional="True" value="10" label="Number of bins per dimension (RT and m/z)" help="(-bins) The higher this value, the more local the intensity significance score is. <br>This parameter should be decreased, if the algorithm is used on small regions of a map"/>
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129 <param name="param_algorithm_mass_trace_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation of peaks belonging to the same mass trace" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/>
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130 <param name="param_algorithm_mass_trace_min_spectra" type="integer" min="1" optional="True" value="10" label="Number of spectra that have to show a similar peak mass in a mass trace" help="(-min_spectra) "/>
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131 <param name="param_algorithm_mass_trace_max_missing" type="integer" min="0" optional="True" value="1" label="Number of consecutive spectra where a high mass deviation or missing peak is acceptable" help="(-max_missing) <br>This parameter should be well below 'min_spectra'!"/>
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132 <param name="param_algorithm_mass_trace_slope_bound" type="float" min="0.0" optional="True" value="0.1" label="The maximum slope of mass trace intensities when extending from the highest peak" help="(-slope_bound) <br>This parameter is important to seperate overlapping elution peaks. <br>It should be increased if feature elution profiles fluctuate a lot"/>
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133 <param name="param_algorithm_isotopic_pattern_charge_low" type="integer" min="1" optional="True" value="1" label="Lowest charge to search fo" help="(-charge_low) "/>
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134 <param name="param_algorithm_isotopic_pattern_charge_high" type="integer" min="1" optional="True" value="4" label="Highest charge to search fo" help="(-charge_high) "/>
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135 <param name="param_algorithm_isotopic_pattern_mz_tolerance" type="float" min="0.0" optional="True" value="0.03" label="Tolerated m/z deviation from the theoretical isotopic pattern" help="(-mz_tolerance) <br>It should be larger than the m/z resolution of the instrument. <br>This value must be smaller than that 1/charge_high!"/>
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136 <param name="param_algorithm_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum seed score a peak has to reach to be used as seed" help="(-min_score) <br>The seed score is the geometric mean of intensity score, mass trace score and isotope pattern score. <br>If your features show a large deviation from the averagene isotope distribution or from an gaussian elution profile, lower this score"/>
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137 <param name="param_algorithm_feature_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="Feature score threshold for a feature to be reported" help="(-min_score) <br>The feature score is the geometric mean of the average relative deviation and the correlation between the model and the observed peaks"/>
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138 <param name="param_algorithm_feature_reported_mz" type="select" optional="True" value="monoisotopic" label="The mass type that is reported for features" help="(-reported_mz) <br>'maximum' returns the m/z value of the highest mass trace. <br>'average' returns the intensity-weighted average m/z value of all contained peaks. <br>'monoisotopic' returns the monoisotopic m/z value derived from the fitted isotope model">
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139 <option value="maximum">maximum</option>
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140 <option value="average">average</option>
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141 <option value="monoisotopic">monoisotopic</option>
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142 </param>
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143 <param name="param_algorithm_user_seed_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Allowed RT deviation of seeds from the user-specified seed position" help="(-rt_tolerance) "/>
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144 <param name="param_algorithm_user_seed_mz_tolerance" type="float" min="0.0" optional="True" value="1.1" label="Allowed m/z deviation of seeds from the user-specified seed position" help="(-mz_tolerance) "/>
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145 <param name="param_algorithm_user_seed_min_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Overwrites 'seed:min_score' for user-specified seeds" help="(-min_score) The cutoff is typically a bit lower in this case"/>
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146 <expand macro="advanced_options">
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147 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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148 <param name="param_algorithm_debug_pseudo_rt_shift" type="float" min="1.0" optional="True" value="500.0" label="Pseudo RT shift used when" help="(-pseudo_rt_shift) "/>
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149 <param name="param_algorithm_isotopic_pattern_intensity_percentage" type="float" min="0.0" max="100.0" optional="True" value="10.0" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity must be present" help="(-intensity_percentage) "/>
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150 <param name="param_algorithm_isotopic_pattern_intensity_percentage_optional" type="float" min="0.0" max="100.0" optional="True" value="0.1" label="Isotopic peaks that contribute more than this percentage to the overall isotope pattern intensity can be missing" help="(-intensity_percentage_optional) "/>
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151 <param name="param_algorithm_isotopic_pattern_optional_fit_improvement" type="float" min="0.0" max="100.0" optional="True" value="2.0" label="Minimal percental improvement of isotope fit to allow leaving out an optional peak" help="(-optional_fit_improvement) "/>
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152 <param name="param_algorithm_isotopic_pattern_mass_window_width" type="float" min="1.0" max="200.0" optional="True" value="25.0" label="Window width in Dalton for precalculation of estimated isotope distributions" help="(-mass_window_width) "/>
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153 <param name="param_algorithm_isotopic_pattern_abundance_12C" type="float" min="0.0" max="100.0" optional="True" value="98.93" label="Rel" help="(-abundance_12C) abundance of the light carbon. Modify if labeled"/>
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154 <param name="param_algorithm_isotopic_pattern_abundance_14N" type="float" min="0.0" max="100.0" optional="True" value="99.632" label="Rel" help="(-abundance_14N) abundance of the light nitrogen. Modify if labeled"/>
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155 <param name="param_algorithm_fit_max_iterations" type="integer" min="1" optional="True" value="500" label="Maximum number of iterations of the fit" help="(-max_iterations) "/>
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156 <param name="param_algorithm_feature_min_isotope_fit" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Minimum isotope fit of the feature before model fitting" help="(-min_isotope_fit) "/>
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157 <param name="param_algorithm_feature_min_trace_score" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Trace score threshold" help="(-min_trace_score) <br>Traces below this threshold are removed after the model fitting. <br>This parameter is important for features that overlap in m/z dimension"/>
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158 <param name="param_algorithm_feature_min_rt_span" type="float" min="0.0" max="1.0" optional="True" value="0.333" label="Minimum RT span in relation to extended area that has to remain after model fitting" help="(-min_rt_span) "/>
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159 <param name="param_algorithm_feature_max_rt_span" type="float" min="0.5" optional="True" value="2.5" label="Maximum RT span in relation to extended area that the model is allowed to have" help="(-max_rt_span) "/>
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160 <param name="param_algorithm_feature_rt_shape" type="select" optional="True" value="symmetric" label="Choose model used for RT profile fitting" help="(-rt_shape) If set to symmetric a gauss shape is used, in case of asymmetric an EGH shape is used">
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161 <option value="symmetric">symmetric</option>
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162 <option value="asymmetric">asymmetric</option>
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163 </param>
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164 <param name="param_algorithm_feature_max_intersection" type="float" min="0.0" max="1.0" optional="True" value="0.35" label="Maximum allowed intersection of features" help="(-max_intersection) "/>
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165 </expand>
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166 </inputs>
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167 <outputs>
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168 <data name="param_out" format="featurexml"/>
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169 <data name="param_out_mzq" format="mzq"/>
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170 </outputs>
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171 <help>**What it does**
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172
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173 Detects two-dimensional features in LC-MS data.
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174
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175
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176 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderCentroided.html</help>
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177 <expand macro="references"/>
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178 </tool>
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