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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="TOFCalibration" name="TOFCalibration" version="2.0.0">
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3 <description>Applies time of flight calibration.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">TOFCalibration</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>TOFCalibration
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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_ext_calibrants:
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19 -ext_calibrants $param_ext_calibrants
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20 #end if
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21 #if $param_ref_masses:
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22 -ref_masses $param_ref_masses
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23 #end if
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24 #if $param_tof_const:
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25 -tof_const $param_tof_const
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26 #end if
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27 #if $param_peak_data:
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28 -peak_data
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $param_algorithm_PeakPicker_signal_to_noise:
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32 -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise
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33 #end if
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34 #if $param_algorithm_PeakPicker_peak_width:
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35 -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width
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36 #end if
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37 #if $param_algorithm_PeakPicker_estimate_peak_width:
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38 -algorithm:PeakPicker:estimate_peak_width
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39 #end if
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40 #if $adv_opts.adv_opts_selector=='advanced':
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41 #if $adv_opts.param_force:
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42 -force
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43 #end if
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44 #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage:
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45 -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage
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46 #end if
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47 #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor:
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48 -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor
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49 #end if
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50 #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor:
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51 -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor
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52 #end if
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53 #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations:
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54 -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations
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55 #end if
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56 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position:
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57 -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position
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58 #end if
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59 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width:
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60 -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width
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61 #end if
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62 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width:
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63 -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width
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64 #end if
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65 #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height:
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66 -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height
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67 #end if
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68 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz:
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69 -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz
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70 #end if
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71 #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance:
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72 -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance
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73 #end if
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74 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound:
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75 -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound
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76 #end if
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77 #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level:
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78 -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level
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79 #end if
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80 #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation:
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81 -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation
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82 #end if
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83 #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level:
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84 -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level
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85 #end if
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86 #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius:
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87 -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius
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88 #end if
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89 #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing:
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90 -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing
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91 #end if
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92 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution:
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93 -algorithm:PeakPicker:deconvolution:deconvolution
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94 #end if
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95 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold:
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96 -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold
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97 #end if
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98 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width:
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99 -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width
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100 #end if
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101 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width:
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102 -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width
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103 #end if
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104 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling:
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105 -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling
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106 #end if
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107 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold:
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108 -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold
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109 #end if
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110 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs:
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111 -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs
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112 #end if
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113 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel:
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114 -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel
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115 #end if
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116 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration:
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117 -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration
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118 #end if
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119 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position:
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120 -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position
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121 #end if
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122 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height:
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123 -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height
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124 #end if
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125 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width:
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126 -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width
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127 #end if
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128 #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width:
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129 -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width
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130 #end if
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131 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity:
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132 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity
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133 #end if
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134 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor:
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135 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor
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136 #end if
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137 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile:
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138 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile
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139 #end if
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140 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode:
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141 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode
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142 #end if
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143 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len:
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144 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len
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145 #end if
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146 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count:
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147 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count
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148 #end if
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149 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp:
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150 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp
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151 #end if
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152 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements:
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153 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements
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154 #end if
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155 #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window:
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156 -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window
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157 #end if
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158 #end if
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159 </command>
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160 <inputs>
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161 <param name="param_in" type="data" format="mzml" optional="False" label="input peak or raw data file" help="(-in) "/>
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162 <param name="param_ext_calibrants" type="data" format="mzml" optional="False" label="input file containing the external calibrant spectra (peak or raw data)" help="(-ext_calibrants) "/>
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163 <param name="param_ref_masses" type="data" format="txt" optional="False" label="input file containing reference masses of the external calibrant spectra (one per line)" help="(-ref_masses) "/>
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164 <param name="param_tof_const" type="data" format="tabular" optional="False" label="File containing TOF conversion constants" help="(-tof_const) These can be either two or three constants <br>per set, depending on the conversion type. Either one set for all calibrant spectra <br>(tab separated), or one for each spectrum. <br>For a detailed description, please have a look at the doxygen documentation.(one set, tab separated, per line)"/>
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165 <param name="param_peak_data" type="boolean" truevalue="-peak_data" falsevalue="" checked="false" optional="True" label="set this flag, if you have peak data, not raw data (the picking parameters are accessible only from the INI file)" help="(-peak_data) "/>
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166 <param name="param_algorithm_PeakPicker_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Minimal signal to noise ratio for a peak to be picked" help="(-signal_to_noise) "/>
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167 <param name="param_algorithm_PeakPicker_peak_width" type="float" min="0.0" optional="True" value="0.15" label="Approximate fwhm of the peaks" help="(-peak_width) "/>
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168 <param name="param_algorithm_PeakPicker_estimate_peak_width" type="boolean" truevalue="-algorithm:PeakPicker:estimate_peak_width" falsevalue="" checked="false" optional="True" label="Flag if the average peak width shall be estimated" help="(-estimate_peak_width) Attention: when this flag is set, the peak_width is ignored"/>
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169 <expand macro="advanced_options">
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170 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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171 <param name="param_algorithm_PeakPicker_centroid_percentage" type="float" min="0.0" max="1.0" optional="True" value="0.8" label="Percentage of the maximum height that the raw data points must exceed to be taken into account for the calculation of the centroid" help="(-centroid_percentage) If it is 1 the centroid position corresponds to the position of the highest intensity"/>
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172 <param name="param_algorithm_PeakPicker_fwhm_lower_bound_factor" type="float" min="0.0" optional="True" value="0.7" label="Factor that calculates the minimal fwhm value from the peak_width" help="(-fwhm_lower_bound_factor) All peaks with width smaller than fwhm_bound_factor * peak_width are discarded"/>
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173 <param name="param_algorithm_PeakPicker_fwhm_upper_bound_factor" type="float" min="0.0" optional="True" value="20.0" label="Factor that calculates the maximal fwhm value from the peak_width" help="(-fwhm_upper_bound_factor) All peaks with width greater than fwhm_upper_bound_factor * peak_width are discarded"/>
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174 <param name="param_algorithm_PeakPicker_optimization_iterations" type="integer" min="1" optional="True" value="400" label="maximal number of iterations for the fitting step" help="(-iterations) "/>
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175 <param name="param_algorithm_PeakPicker_optimization_penalties_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the position:If it differs too much from the initial one it can be penalized" help="(-position) "/>
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176 <param name="param_algorithm_PeakPicker_optimization_penalties_left_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the left width:If the left width differs too much from the initial one during the fitting it can be penalized" help="(-left_width) "/>
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177 <param name="param_algorithm_PeakPicker_optimization_penalties_right_width" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the right width:If the right width differs too much from the initial one during the fitting it can be penalized" help="(-right_width) "/>
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178 <param name="param_algorithm_PeakPicker_optimization_penalties_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity (only used in 2D Optimization):If it gets negative during the fitting it can be penalized" help="(-height) "/>
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179 <param name="param_algorithm_PeakPicker_optimization_2d_tolerance_mz" type="float" min="0.0" optional="True" value="2.2" label="mz tolerance for cluster construction" help="(-tolerance_mz) "/>
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180 <param name="param_algorithm_PeakPicker_optimization_2d_max_peak_distance" type="float" min="0.0" optional="True" value="1.2" label="maximal peak distance in mz in a cluste" help="(-max_peak_distance) "/>
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181 <param name="param_algorithm_PeakPicker_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/>
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182 <param name="param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity for MS/MS peaks" help="(-peak_bound_ms2_level) "/>
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183 <param name="param_algorithm_PeakPicker_thresholds_correlation" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="minimal correlation of a peak and the raw signal" help="(-correlation) If a peak has a lower correlation it is skipped"/>
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184 <param name="param_algorithm_PeakPicker_thresholds_noise_level" type="float" min="0.0" optional="True" value="0.1" label="noise level for the search of the peak endpoints" help="(-noise_level) "/>
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185 <param name="param_algorithm_PeakPicker_thresholds_search_radius" type="integer" min="0" optional="True" value="3" label="search radius for the search of the maximum in the signal after a maximum in the cwt was found" help="(-search_radius) "/>
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186 <param name="param_algorithm_PeakPicker_wavelet_transform_spacing" type="float" min="0.0" optional="True" value="0.001" label="spacing of the cwt" help="(-spacing) "/>
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187 <param name="param_algorithm_PeakPicker_deconvolution_deconvolution" type="boolean" truevalue="-algorithm:PeakPicker:deconvolution:deconvolution" falsevalue="" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to "true"" help="(-deconvolution) "/>
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188 <param name="param_algorithm_PeakPicker_deconvolution_asym_threshold" type="float" min="0.0" optional="True" value="0.3" label="If the symmetry of a peak is smaller than asym_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help="(-asym_threshold) "/>
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189 <param name="param_algorithm_PeakPicker_deconvolution_left_width" type="float" min="0.0" optional="True" value="2.0" label="1/left_width is the initial value for the left width of the peaks found in the deconvolution step" help="(-left_width) "/>
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190 <param name="param_algorithm_PeakPicker_deconvolution_right_width" type="float" min="0.0" optional="True" value="2.0" label="1/right_width is the initial value for the right width of the peaks found in the deconvolution step" help="(-right_width) "/>
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191 <param name="param_algorithm_PeakPicker_deconvolution_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the seperation of heavily overlapping peaks" help="(-scaling) The initial value is used for charge 1, for higher charges it is adapted to scaling/charge"/>
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192 <param name="param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold" type="float" min="0.0" optional="True" value="0.7" label="If the fwhm of a peak is higher than fwhm_thresholds it is assumed that it consists of more than one peak and the deconvolution procedure is started" help="(-fwhm_threshold) "/>
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193 <param name="param_algorithm_PeakPicker_deconvolution_fitting_eps_abs" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the absolute error gets smaller than this value the fitting is stopped" help="(-eps_abs) "/>
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194 <param name="param_algorithm_PeakPicker_deconvolution_fitting_eps_rel" type="float" min="0.0" optional="True" value="9.99999974738e-06" label="if the relative error gets smaller than this value the fitting is stopped" help="(-eps_rel) "/>
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195 <param name="param_algorithm_PeakPicker_deconvolution_fitting_max_iteration" type="integer" min="1" optional="True" value="10" label="maximal number of iterations for the fitting step" help="(-max_iteration) "/>
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196 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_position" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the peak position:If the position changes more than 0.5Da during the fitting it can be penalized as well as discrepancies of the peptide mass rule" help="(-position) "/>
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197 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_height" type="float" min="0.0" optional="True" value="1.0" label="penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized" help="(-height) "/>
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198 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized" help="(-left_width) "/>
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199 <param name="param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width" type="float" min="0.0" optional="True" value="0.0" label="penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized" help="(-right_width) "/>
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200 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will not be added to the histogram. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime)"/>
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201 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/>
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202 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/>
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203 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --> use 'max_intensity'; 0 --> 'auto_max_stdev_factor' method (default); 1 --> 'auto_max_percentile' method" help="(-auto_mode) "/>
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204 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
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205 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
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206 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp" type="float" min="0.01" max="999.0" optional="True" value="3.0" label="multiplier for stdev" help="(-stdev_mp) "/>
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207 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/>
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208 <param name="param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/>
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209 </expand>
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210 </inputs>
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211 <outputs>
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212 <data name="param_out" format="mzml"/>
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213 </outputs>
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214 <help>**What it does**
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215
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216 Applies time of flight calibration.
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217
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218
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219 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html</help>
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220 <expand macro="references"/>
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221 </tool>
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