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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathAnalyzer" name="OpenSwathAnalyzer" version="2.0.0">
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3 <description>Picks peaks and finds features in an SRM experiment.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathAnalyzer</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>OpenSwathAnalyzer
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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_tr:
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16 -tr $param_tr
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17 #end if
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18 #if $param_rt_norm:
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19 -rt_norm $param_rt_norm
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_no_strict:
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25 -no-strict
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26 #end if
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27 -swath_files
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28 #for token in $param_swath_files:
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29 $token
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30 #end for
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31 #if $param_min_upper_edge_dist:
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32 -min_upper_edge_dist $param_min_upper_edge_dist
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33 #end if
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34 -threads \${GALAXY_SLOTS:-24}
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35 #if $param_algorithm_stop_report_after_feature:
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36 -algorithm:stop_report_after_feature $param_algorithm_stop_report_after_feature
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37 #end if
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38 #if $param_algorithm_rt_extraction_window:
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39 -algorithm:rt_extraction_window $param_algorithm_rt_extraction_window
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40 #end if
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41 #if $param_algorithm_rt_normalization_factor:
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42 -algorithm:rt_normalization_factor $param_algorithm_rt_normalization_factor
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43 #end if
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44 #if $param_algorithm_TransitionGroupPicker_stop_after_feature:
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45 -algorithm:TransitionGroupPicker:stop_after_feature $param_algorithm_TransitionGroupPicker_stop_after_feature
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46 #end if
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47 #if $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio:
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48 -algorithm:TransitionGroupPicker:stop_after_intensity_ratio $param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio
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49 #end if
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50 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
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51 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
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52 #end if
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53 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
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54 -algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
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55 #end if
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56 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width:
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57 -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
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58 #end if
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59 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
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60 -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
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61 #end if
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62 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
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63 -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
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64 #end if
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65 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
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66 -algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
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67 #end if
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68 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len:
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69 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len
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70 #end if
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71 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count:
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72 -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
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73 #end if
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74 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
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75 -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
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76 #end if
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77 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
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78 -algorithm:TransitionGroupPicker:PeakPickerMRM:method
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79 #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
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80 "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
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81 #else
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82 $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
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83 #end if
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84 #end if
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85 #if $param_algorithm_DIAScoring_dia_extraction_window:
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86 -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
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87 #end if
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88 #if $param_algorithm_DIAScoring_dia_centroided:
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89 -algorithm:DIAScoring:dia_centroided
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90 #end if
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91 #if $param_algorithm_DIAScoring_dia_byseries_intensity_min:
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92 -algorithm:DIAScoring:dia_byseries_intensity_min $param_algorithm_DIAScoring_dia_byseries_intensity_min
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93 #end if
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94 #if $param_algorithm_DIAScoring_dia_byseries_ppm_diff:
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95 -algorithm:DIAScoring:dia_byseries_ppm_diff $param_algorithm_DIAScoring_dia_byseries_ppm_diff
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96 #end if
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97 #if $param_algorithm_DIAScoring_dia_nr_isotopes:
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98 -algorithm:DIAScoring:dia_nr_isotopes $param_algorithm_DIAScoring_dia_nr_isotopes
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99 #end if
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100 #if $param_algorithm_DIAScoring_dia_nr_charges:
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101 -algorithm:DIAScoring:dia_nr_charges $param_algorithm_DIAScoring_dia_nr_charges
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102 #end if
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103 #if $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff:
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104 -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
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105 #end if
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106 #if $adv_opts.adv_opts_selector=='advanced':
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107 #if $adv_opts.param_force:
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108 -force
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109 #end if
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110 #if $adv_opts.param_model_type:
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111 -model:type
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112 #if " " in str($adv_opts.param_model_type):
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113 "$adv_opts.param_model_type"
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114 #else
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115 $adv_opts.param_model_type
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116 #end if
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117 #end if
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118 #if $adv_opts.param_model_symmetric_regression:
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119 -model:symmetric_regression
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120 #end if
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121 #if $adv_opts.param_algorithm_quantification_cutoff:
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122 -algorithm:quantification_cutoff $adv_opts.param_algorithm_quantification_cutoff
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123 #end if
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124 #if $adv_opts.param_algorithm_write_convex_hull:
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125 -algorithm:write_convex_hull
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126 #end if
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127 #if $adv_opts.param_algorithm_add_up_spectra:
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128 -algorithm:add_up_spectra $adv_opts.param_algorithm_add_up_spectra
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129 #end if
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130 #if $adv_opts.param_algorithm_spacing_for_spectra_resampling:
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131 -algorithm:spacing_for_spectra_resampling $adv_opts.param_algorithm_spacing_for_spectra_resampling
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132 #end if
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133 #if $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width:
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134 -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
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135 #end if
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136 #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
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137 -algorithm:TransitionGroupPicker:background_subtraction
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138 #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
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139 "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
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140 #else
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141 $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
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142 #end if
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143 #end if
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144 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
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145 -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
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146 #end if
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147 #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z:
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148 -algorithm:TransitionGroupPicker:recalculate_peaks_max_z $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z
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149 #end if
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150 #if $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality:
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151 -algorithm:TransitionGroupPicker:minimal_quality $adv_opts.param_algorithm_TransitionGroupPicker_minimal_quality
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152 #end if
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153 #if $adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality:
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154 -algorithm:TransitionGroupPicker:compute_peak_quality "$adv_opts.param_algorithm_TransitionGroupPicker_compute_peak_quality"
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155 #end if
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156 #if $adv_opts.param_algorithm_EMGScoring_interpolation_step:
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157 -algorithm:EMGScoring:interpolation_step $adv_opts.param_algorithm_EMGScoring_interpolation_step
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158 #end if
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159 #if $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box:
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160 -algorithm:EMGScoring:tolerance_stdev_bounding_box $adv_opts.param_algorithm_EMGScoring_tolerance_stdev_bounding_box
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161 #end if
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162 #if $adv_opts.param_algorithm_EMGScoring_max_iteration:
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163 -algorithm:EMGScoring:max_iteration $adv_opts.param_algorithm_EMGScoring_max_iteration
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164 #end if
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165 #if $adv_opts.param_algorithm_EMGScoring_statistics_mean:
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166 -algorithm:EMGScoring:statistics:mean $adv_opts.param_algorithm_EMGScoring_statistics_mean
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167 #end if
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168 #if $adv_opts.param_algorithm_EMGScoring_statistics_variance:
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169 -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
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170 #end if
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171 #if $adv_opts.param_algorithm_Scores_use_shape_score:
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172 -algorithm:Scores:use_shape_score
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173 #end if
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174 #if $adv_opts.param_algorithm_Scores_use_coelution_score:
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175 -algorithm:Scores:use_coelution_score
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176 #end if
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177 #if $adv_opts.param_algorithm_Scores_use_rt_score:
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178 -algorithm:Scores:use_rt_score
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179 #end if
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180 #if $adv_opts.param_algorithm_Scores_use_library_score:
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181 -algorithm:Scores:use_library_score
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182 #end if
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183 #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
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184 -algorithm:Scores:use_elution_model_score
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185 #end if
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186 #if $adv_opts.param_algorithm_Scores_use_intensity_score:
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187 -algorithm:Scores:use_intensity_score
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188 #end if
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189 #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
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190 -algorithm:Scores:use_nr_peaks_score
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191 #end if
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192 #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
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193 -algorithm:Scores:use_total_xic_score
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194 #end if
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195 #if $adv_opts.param_algorithm_Scores_use_sn_score:
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196 -algorithm:Scores:use_sn_score
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197 #end if
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198 #if $adv_opts.param_algorithm_Scores_use_dia_scores:
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199 -algorithm:Scores:use_dia_scores
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200 #end if
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201 #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
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202 -algorithm:Scores:use_ms1_correlation
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203 #end if
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204 #if $adv_opts.param_algorithm_Scores_use_ms1_fullscan:
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205 -algorithm:Scores:use_ms1_fullscan
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206 #end if
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207 #end if
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208 </command>
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209 <inputs>
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210 <param name="param_in" type="data" format="mzml" optional="False" label="input file containing the chromatograms" help="(-in) "/>
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211 <param name="param_tr" type="data" format="traml" optional="False" label="transition file" help="(-tr) "/>
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212 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
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213 <param name="param_no_strict" type="boolean" truevalue="-no-strict" falsevalue="" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped" help="(-no-strict) "/>
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214 <param name="param_swath_files" type="data" format="mzml" multiple="true" optional="True" size="30" label="[applies only if you have full MS2 spectra maps] Swath files that were used to extract the transitions" help="(-swath_files) If present, SWATH specific scoring will be used">
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215 <sanitizer>
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216 <valid initial="string.printable">
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217 <remove value="'"/>
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218 <remove value="""/>
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219 </valid>
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220 </sanitizer>
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221 </param>
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222 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="[applies only if you have full MS2 spectra maps] Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help="(-min_upper_edge_dist) "/>
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223 <param name="param_algorithm_stop_report_after_feature" type="integer" value="-1" label="Stop reporting after feature (ordered by quality; -1 means do not stop)" help="(-stop_report_after_feature) "/>
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224 <param name="param_algorithm_rt_extraction_window" type="float" value="-1.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 500 means to extract around +/- 500 s of the expected elution)" help="(-rt_extraction_window) For this to work, the TraML input file needs to contain normalized RT values"/>
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225 <param name="param_algorithm_rt_normalization_factor" type="float" value="1.0" label="The normalized RT is expected to be between 0 and 1. If your normalized RT has a different range, pass this here (" help="(-rt_normalization_factor) e.g. it goes from 0 to 100, set this value to 100)"/>
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226 <param name="param_algorithm_TransitionGroupPicker_stop_after_feature" type="integer" value="-1" label="Stop finding after feature (ordered by intensity; -1 means do not stop)" help="(-stop_after_feature) "/>
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227 <param name="param_algorithm_TransitionGroupPicker_stop_after_intensity_ratio" type="float" value="0.0001" label="Stop after reaching intensity ratio" help="(-stop_after_intensity_ratio) "/>
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228 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="15" label="The number of subsequent data points used for smoothing" help="(-sgolay_frame_length) <br>This number has to be uneven. If it is not, 1 will be added"/>
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229 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order" type="integer" value="3" label="Order of the polynomial that is fitted" help="(-sgolay_polynomial_order) "/>
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230 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="50.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
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231 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="true" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
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232 <sanitizer>
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233 <valid initial="string.printable">
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234 <remove value="'"/>
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235 <remove value="""/>
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236 </valid>
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237 </sanitizer>
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238 </param>
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239 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="40.0" label="Force a certain minimal peak_width on the data (" help="(-peak_width) e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off"/>
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240 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="1.0" label="Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (" help="(-signal_to_noise) e.g. 1.0) can lead to peaks whose flanks are not fully captured"/>
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241 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_win_len" type="float" value="1000.0" label="Signal to noise window length" help="(-sn_win_len) "/>
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242 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count" type="integer" value="30" label="Signal to noise bin count" help="(-sn_bin_count) "/>
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243 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="false" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
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244 <param name="param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="legacy" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
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245 <option value="legacy">legacy</option>
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246 <option value="corrected">corrected</option>
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247 <option value="crawdad">crawdad</option>
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248 </param>
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249 <param name="param_algorithm_DIAScoring_dia_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="DIA extraction window in Th" help="(-dia_extraction_window) "/>
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250 <param name="param_algorithm_DIAScoring_dia_centroided" type="boolean" truevalue="-algorithm:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
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251 <param name="param_algorithm_DIAScoring_dia_byseries_intensity_min" type="float" min="0.0" optional="True" value="300.0" label="DIA b/y series minimum intensity to conside" help="(-dia_byseries_intensity_min) "/>
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252 <param name="param_algorithm_DIAScoring_dia_byseries_ppm_diff" type="float" min="0.0" optional="True" value="10.0" label="DIA b/y series minimal difference in ppm to conside" help="(-dia_byseries_ppm_diff) "/>
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253 <param name="param_algorithm_DIAScoring_dia_nr_isotopes" type="integer" min="0" optional="True" value="4" label="DIA nr of isotopes to conside" help="(-dia_nr_isotopes) "/>
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254 <param name="param_algorithm_DIAScoring_dia_nr_charges" type="integer" min="0" optional="True" value="4" label="DIA nr of charges to conside" help="(-dia_nr_charges) "/>
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255 <param name="param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff" type="float" min="0.0" optional="True" value="20.0" label="DIA maximal difference in ppm to count a peak at lower m/z when searching for evidence that a peak might not be monoisotopic" help="(-peak_before_mono_max_ppm_diff) "/>
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256 <expand macro="advanced_options">
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257 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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258 <param name="param_model_type" type="select" optional="True" value="linear" label="Type of model" help="(-type) ">
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259 <option value="linear">linear</option>
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260 <option value="b_spline">b_spline</option>
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261 <option value="interpolated">interpolated</option>
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262 </param>
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263 <param name="param_model_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
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264 <param name="param_algorithm_quantification_cutoff" type="float" min="0.0" optional="True" value="0.0" label="Cutoff in m/z below which peaks should not be used for quantification any more" help="(-quantification_cutoff) "/>
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265 <param name="param_algorithm_write_convex_hull" type="boolean" truevalue="-algorithm:write_convex_hull" falsevalue="" checked="false" optional="True" label="Whether to write out all points of all features into the featureXML" help="(-write_convex_hull) "/>
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266 <param name="param_algorithm_add_up_spectra" type="integer" min="1" optional="True" value="1" label="Add up spectra around the peak apex (needs to be a non-even integer)" help="(-add_up_spectra) "/>
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267 <param name="param_algorithm_spacing_for_spectra_resampling" type="float" min="0.0" optional="True" value="0.005" label="If spectra are to be added, use this spacing to add them up" help="(-spacing_for_spectra_resampling) "/>
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268 <param name="param_algorithm_TransitionGroupPicker_min_peak_width" type="float" value="-1.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
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269 <param name="param_algorithm_TransitionGroupPicker_background_subtraction" type="select" optional="True" value="none" label="Try to apply a background subtraction to the peak (experimental)" help="(-background_subtraction) The background is estimated at the peak boundaries, either the smoothed or the raw chromatogram data can be used for that">
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270 <option value="none">none</option>
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271 <option value="smoothed">smoothed</option>
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272 <option value="original">original</option>
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273 </param>
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274 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="false" label="Tries to get better peak picking by looking at peak consistency of all picked peaks" help="(-recalculate_peaks) Tries to use the consensus (median) peak border if theof variation within the picked peaks is too large">
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275 <sanitizer>
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276 <valid initial="string.printable">
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277 <remove value="'"/>
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278 <remove value="""/>
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279 </valid>
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280 </sanitizer>
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281 </param>
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282 <param name="param_algorithm_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="1.0" label="Determines the maximal Z-Score (difference measured in standard deviations) that is considered too large for peak boundaries" help="(-recalculate_peaks_max_z) If the Z-Score is above this value, the median is used for peak boundaries (default value 1.0)"/>
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283 <param name="param_algorithm_TransitionGroupPicker_minimal_quality" type="float" value="-10000.0" label="Only if compute_peak_quality is set, this parameter will not consider peaks below this quality threshold" help="(-minimal_quality) "/>
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284 <param name="param_algorithm_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="false" label="Tries to compute a quality value for each peakgroup and detect outlier transitions" help="(-compute_peak_quality) The resulting score is centered around zero and values above 0 are generally good and below -1 or -2 are usually bad">
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285 <sanitizer>
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286 <valid initial="string.printable">
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287 <remove value="'"/>
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288 <remove value="""/>
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289 </valid>
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290 </sanitizer>
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291 </param>
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292 <param name="param_algorithm_EMGScoring_interpolation_step" type="float" value="0.2" label="Sampling rate for the interpolation of the model function" help="(-interpolation_step) "/>
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293 <param name="param_algorithm_EMGScoring_tolerance_stdev_bounding_box" type="float" value="3.0" label="Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data" help="(-tolerance_stdev_bounding_box) "/>
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294 <param name="param_algorithm_EMGScoring_max_iteration" type="integer" value="500" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
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295 <param name="param_algorithm_EMGScoring_statistics_mean" type="float" value="1.0" label="Centroid position of the model" help="(-mean) "/>
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296 <param name="param_algorithm_EMGScoring_statistics_variance" type="float" value="1.0" label="Variance of the model" help="(-variance) "/>
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297 <param name="param_algorithm_Scores_use_shape_score" type="boolean" truevalue="-algorithm:Scores:use_shape_score" falsevalue="" checked="true" optional="True" label="Use the shape score (this score measures the similarity in shape of the transitions using a cross-correlation)" help="(-use_shape_score) "/>
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298 <param name="param_algorithm_Scores_use_coelution_score" type="boolean" truevalue="-algorithm:Scores:use_coelution_score" falsevalue="" checked="true" optional="True" label="Use the coelution score (this score measures the similarity in coelution of the transitions using a cross-correlation)" help="(-use_coelution_score) "/>
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299 <param name="param_algorithm_Scores_use_rt_score" type="boolean" truevalue="-algorithm:Scores:use_rt_score" falsevalue="" checked="true" optional="True" label="Use the retention time score (this score measure the difference in retention time)" help="(-use_rt_score) "/>
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300 <param name="param_algorithm_Scores_use_library_score" type="boolean" truevalue="-algorithm:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/>
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301 <param name="param_algorithm_Scores_use_elution_model_score" type="boolean" truevalue="-algorithm:Scores:use_elution_model_score" falsevalue="" checked="true" optional="True" label="Use the elution model (EMG) score (this score fits a gaussian model to the peak and checks the fit)" help="(-use_elution_model_score) "/>
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302 <param name="param_algorithm_Scores_use_intensity_score" type="boolean" truevalue="-algorithm:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/>
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303 <param name="param_algorithm_Scores_use_nr_peaks_score" type="boolean" truevalue="-algorithm:Scores:use_nr_peaks_score" falsevalue="" checked="true" optional="True" label="Use the number of peaks score" help="(-use_nr_peaks_score) "/>
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304 <param name="param_algorithm_Scores_use_total_xic_score" type="boolean" truevalue="-algorithm:Scores:use_total_xic_score" falsevalue="" checked="true" optional="True" label="Use the total XIC score" help="(-use_total_xic_score) "/>
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305 <param name="param_algorithm_Scores_use_sn_score" type="boolean" truevalue="-algorithm:Scores:use_sn_score" falsevalue="" checked="true" optional="True" label="Use the SN (signal to noise) score" help="(-use_sn_score) "/>
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306 <param name="param_algorithm_Scores_use_dia_scores" type="boolean" truevalue="-algorithm:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/>
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307 <param name="param_algorithm_Scores_use_ms1_correlation" type="boolean" truevalue="-algorithm:Scores:use_ms1_correlation" falsevalue="" checked="false" optional="True" label="Use the correlation scores with the MS1 elution profiles" help="(-use_ms1_correlation) "/>
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308 <param name="param_algorithm_Scores_use_ms1_fullscan" type="boolean" truevalue="-algorithm:Scores:use_ms1_fullscan" falsevalue="" checked="false" optional="True" label="Use the full MS1 scan at the peak apex for scoring (ppm accuracy of precursor and isotopic pattern)" help="(-use_ms1_fullscan) "/>
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309 </expand>
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310 </inputs>
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311 <outputs>
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312 <data name="param_out" format="featurexml"/>
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313 </outputs>
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314 <help>**What it does**
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315
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316 Picks peaks and finds features in an SRM experiment.
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317
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318
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319 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathAnalyzer.html</help>
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320 <expand macro="references"/>
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321 </tool>
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