Mercurial > repos > galaxyp > openms_peakpickerwavelet

annotate PeakPickerWavelet.xml @ 3:fa2e65e323dc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600
author galaxyp
date Sat, 28 Oct 2017 05:24:28 -0400
parents 22162ad90646
children 409cec15d717
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4ee66bd832d9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [Signal processing and preprocessing]-->
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4 <tool id="PeakPickerWavelet" name="PeakPickerWavelet" version="2.2.0">
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5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PeakPickerWavelet</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>PeakPickerWavelet
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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 #if $param_algorithm_signal_to_noise:
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22 -algorithm:signal_to_noise $param_algorithm_signal_to_noise
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23 #end if
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24 #if $param_algorithm_peak_width:
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25 -algorithm:peak_width $param_algorithm_peak_width
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26 #end if
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27 #if $param_algorithm_estimate_peak_width:
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28 -algorithm:estimate_peak_width
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29 #end if
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30 #if $adv_opts.adv_opts_selector=='advanced':
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31 #if $adv_opts.param_write_peak_meta_data:
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32 -write_peak_meta_data
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33 #end if
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34 #if $adv_opts.param_force:
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35 -force
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36 #end if
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37 #if $adv_opts.param_algorithm_centroid_percentage:
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38 -algorithm:centroid_percentage $adv_opts.param_algorithm_centroid_percentage
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39 #end if
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40 #if $adv_opts.param_algorithm_fwhm_lower_bound_factor:
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41 -algorithm:fwhm_lower_bound_factor $adv_opts.param_algorithm_fwhm_lower_bound_factor
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42 #end if
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43 #if $adv_opts.param_algorithm_fwhm_upper_bound_factor:
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44 -algorithm:fwhm_upper_bound_factor $adv_opts.param_algorithm_fwhm_upper_bound_factor
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45 #end if
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46 #if $adv_opts.param_algorithm_optimization_iterations:
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47 -algorithm:optimization:iterations $adv_opts.param_algorithm_optimization_iterations
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48 #end if
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49 #if $adv_opts.param_algorithm_optimization_penalties_position:
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50 -algorithm:optimization:penalties:position $adv_opts.param_algorithm_optimization_penalties_position
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51 #end if
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52 #if $adv_opts.param_algorithm_optimization_penalties_left_width:
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53 -algorithm:optimization:penalties:left_width $adv_opts.param_algorithm_optimization_penalties_left_width
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54 #end if
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55 #if $adv_opts.param_algorithm_optimization_penalties_right_width:
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56 -algorithm:optimization:penalties:right_width $adv_opts.param_algorithm_optimization_penalties_right_width
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57 #end if
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58 #if $adv_opts.param_algorithm_optimization_penalties_height:
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59 -algorithm:optimization:penalties:height $adv_opts.param_algorithm_optimization_penalties_height
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60 #end if
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61 #if $adv_opts.param_algorithm_optimization_2d_tolerance_mz:
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62 -algorithm:optimization:2d:tolerance_mz $adv_opts.param_algorithm_optimization_2d_tolerance_mz
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63 #end if
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64 #if $adv_opts.param_algorithm_optimization_2d_max_peak_distance:
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65 -algorithm:optimization:2d:max_peak_distance $adv_opts.param_algorithm_optimization_2d_max_peak_distance
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66 #end if
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67 #if $adv_opts.param_algorithm_thresholds_peak_bound:
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68 -algorithm:thresholds:peak_bound $adv_opts.param_algorithm_thresholds_peak_bound
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69 #end if
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70 #if $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level:
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71 -algorithm:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_thresholds_peak_bound_ms2_level
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72 #end if
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73 #if $adv_opts.param_algorithm_thresholds_correlation:
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74 -algorithm:thresholds:correlation $adv_opts.param_algorithm_thresholds_correlation
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75 #end if
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76 #if $adv_opts.param_algorithm_thresholds_noise_level:
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77 -algorithm:thresholds:noise_level $adv_opts.param_algorithm_thresholds_noise_level
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78 #end if
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79 #if $adv_opts.param_algorithm_thresholds_search_radius:
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80 -algorithm:thresholds:search_radius $adv_opts.param_algorithm_thresholds_search_radius
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81 #end if
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82 #if $adv_opts.param_algorithm_wavelet_transform_spacing:
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83 -algorithm:wavelet_transform:spacing $adv_opts.param_algorithm_wavelet_transform_spacing
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84 #end if
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85 #if $adv_opts.param_algorithm_deconvolution_deconvolution:
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86 -algorithm:deconvolution:deconvolution
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87 #end if
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88 #if $adv_opts.param_algorithm_deconvolution_asym_threshold:
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89 -algorithm:deconvolution:asym_threshold $adv_opts.param_algorithm_deconvolution_asym_threshold
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90 #end if
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91 #if $adv_opts.param_algorithm_deconvolution_left_width:
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92 -algorithm:deconvolution:left_width $adv_opts.param_algorithm_deconvolution_left_width
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93 #end if
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94 #if $adv_opts.param_algorithm_deconvolution_right_width:
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95 -algorithm:deconvolution:right_width $adv_opts.param_algorithm_deconvolution_right_width
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96 #end if
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97 #if $adv_opts.param_algorithm_deconvolution_scaling:
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98 -algorithm:deconvolution:scaling $adv_opts.param_algorithm_deconvolution_scaling
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99 #end if
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100 #if $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold:
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101 -algorithm:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_deconvolution_fitting_fwhm_threshold
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102 #end if
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103 #if $adv_opts.param_algorithm_deconvolution_fitting_eps_abs:
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104 -algorithm:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_deconvolution_fitting_eps_abs
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105 #end if
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106 #if $adv_opts.param_algorithm_deconvolution_fitting_eps_rel:
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107 -algorithm:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_deconvolution_fitting_eps_rel
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108 #end if
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109 #if $adv_opts.param_algorithm_deconvolution_fitting_max_iteration:
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110 -algorithm:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_deconvolution_fitting_max_iteration
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111 #end if
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112 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_position:
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113 -algorithm:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_deconvolution_fitting_penalties_position
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114 #end if
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115 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_height:
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116 -algorithm:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_deconvolution_fitting_penalties_height
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117 #end if
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118 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width:
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119 -algorithm:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_left_width
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120 #end if
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121 #if $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width:
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122 -algorithm:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_deconvolution_fitting_penalties_right_width
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123 #end if
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124 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity:
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125 -algorithm:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_max_intensity
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126 #end if
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127 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor:
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128 -algorithm:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_stdev_factor
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129 #end if
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130 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile:
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131 -algorithm:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_max_percentile
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132 #end if
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133 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode:
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134 -algorithm:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_auto_mode
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135 #end if
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136 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len:
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137 -algorithm:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_win_len
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138 #end if
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139 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count:
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140 -algorithm:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_bin_count
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141 #end if
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142 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp:
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143 -algorithm:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_stdev_mp
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144 #end if
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145 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements:
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146 -algorithm:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_min_required_elements
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147 #end if
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148 #if $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window:
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149 -algorithm:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoiseEstimationParameter_noise_for_empty_window
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150 #end if
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151 #end if
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152 </command>
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153 <inputs>
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154 <param name="param_in" type="data" format="mzml" optional="False" label="input profile data file" help="(-in) "/>
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155 <param name="param_algorithm_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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156 <param name="param_algorithm_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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157 <param name="param_algorithm_estimate_peak_width" display="radio" type="boolean" truevalue="-algorithm: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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158 <expand macro="advanced_options">
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159 <param name="param_write_peak_meta_data" display="radio" type="boolean" truevalue="-write_peak_meta_data" falsevalue="" checked="false" optional="True" label="Write additional information about the picked peaks (maximal intensity, left and right area...) into the mzML-file" help="(-write_peak_meta_data) Attention: this can blow up files, since seven arrays are stored per spectrum!"/>
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160 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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161 <param name="param_algorithm_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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162 <param name="param_algorithm_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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163 <param name="param_algorithm_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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164 <param name="param_algorithm_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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165 <param name="param_algorithm_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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166 <param name="param_algorithm_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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167 <param name="param_algorithm_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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168 <param name="param_algorithm_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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169 <param name="param_algorithm_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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170 <param name="param_algorithm_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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171 <param name="param_algorithm_thresholds_peak_bound" type="float" min="0.0" optional="True" value="10.0" label="Minimal peak intensity" help="(-peak_bound) "/>
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172 <param name="param_algorithm_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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173 <param name="param_algorithm_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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174 <param name="param_algorithm_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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175 <param name="param_algorithm_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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176 <param name="param_algorithm_wavelet_transform_spacing" type="float" min="0.0" optional="True" value="0.001" label="Spacing of the CWT" help="(-spacing) Note that the accuracy of the picked peak's centroid position depends in the Raw data spacing, i.e., 50% of raw peak distance at most"/>
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177 <param name="param_algorithm_deconvolution_deconvolution" display="radio" type="boolean" truevalue="-algorithm:deconvolution:deconvolution" falsevalue="" checked="false" optional="True" label="If you want heavily overlapping peaks to be separated set this value to &quot;true&quot;" help="(-deconvolution) "/>
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178 <param name="param_algorithm_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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179 <param name="param_algorithm_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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180 <param name="param_algorithm_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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181 <param name="param_algorithm_deconvolution_scaling" type="float" min="0.0" optional="True" value="0.12" label="Initial scaling of the cwt used in the separation 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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182 <param name="param_algorithm_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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183 <param name="param_algorithm_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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184 <param name="param_algorithm_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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185 <param name="param_algorithm_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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186 <param name="param_algorithm_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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187 <param name="param_algorithm_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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188 <param name="param_algorithm_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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189 <param name="param_algorithm_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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190 <param name="param_algorithm_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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191 <param name="param_algorithm_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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192 <param name="param_algorithm_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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193 <param name="param_algorithm_SignalToNoiseEstimationParameter_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/>
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194 <param name="param_algorithm_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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195 <param name="param_algorithm_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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196 <param name="param_algorithm_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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197 <param name="param_algorithm_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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198 <param name="param_algorithm_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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199 </expand>
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200 </inputs>
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201 <outputs>
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202 <data name="param_out" format="mzml"/>
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203 </outputs>
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204 <help>Finds mass spectrometric peaks in profile mass spectra.
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205
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206
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207 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PeakPickerWavelet.html</help>
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208 </tool>