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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.0.0">
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3 <description>Complete workflow to run OpenSWATH</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathWorkflow</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>OpenSwathWorkflow
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 #if $param_tr:
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17 -tr $param_tr
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18 #end if
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19 #if $param_tr_type:
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20 -tr_type
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21 #if " " in str($param_tr_type):
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22 "$param_tr_type"
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23 #else
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24 $param_tr_type
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25 #end if
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26 #end if
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27 #if $param_tr_irt:
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28 -tr_irt $param_tr_irt
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29 #end if
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4
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30 #if $output_fmt == 'tsv':
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31 -out_tsv "$out_tsv"
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32 #else:
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33 -out_features "$out_features"
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0
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34 #end if
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35 #if $param_out_chrom:
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36 -out_chrom $param_out_chrom
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37 #end if
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38 #if $param_rt_extraction_window:
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39 -rt_extraction_window $param_rt_extraction_window
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40 #end if
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41 #if $param_mz_extraction_window:
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42 -mz_extraction_window $param_mz_extraction_window
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43 #end if
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44 #if $param_ppm:
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45 -ppm
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46 #end if
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47 -threads \${GALAXY_SLOTS:-24}
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48 #if $param_Scoring_stop_report_after_feature:
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49 -Scoring:stop_report_after_feature $param_Scoring_stop_report_after_feature
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50 #end if
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51 #if $param_Scoring_rt_normalization_factor:
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52 -Scoring:rt_normalization_factor $param_Scoring_rt_normalization_factor
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53 #end if
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54 #if $param_Scoring_TransitionGroupPicker_stop_after_feature:
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55 -Scoring:TransitionGroupPicker:stop_after_feature $param_Scoring_TransitionGroupPicker_stop_after_feature
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56 #end if
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57 #if $param_Scoring_TransitionGroupPicker_min_peak_width:
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58 -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
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59 #end if
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60 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
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61 -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
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62 #end if
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63 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z:
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64 -Scoring:TransitionGroupPicker:recalculate_peaks_max_z $param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z
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65 #end if
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66 #if $param_Scoring_TransitionGroupPicker_minimal_quality:
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67 -Scoring:TransitionGroupPicker:minimal_quality $param_Scoring_TransitionGroupPicker_minimal_quality
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68 #end if
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69 #if $param_Scoring_TransitionGroupPicker_compute_peak_quality:
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70 -Scoring:TransitionGroupPicker:compute_peak_quality "$param_Scoring_TransitionGroupPicker_compute_peak_quality"
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71 #end if
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72 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length:
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73 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length
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74 #end if
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75 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order:
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76 -Scoring:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order $param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_polynomial_order
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77 #end if
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78 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width:
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79 -Scoring:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width
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80 #end if
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81 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss:
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82 -Scoring:TransitionGroupPicker:PeakPickerMRM:use_gauss "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss"
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83 #end if
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84 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width:
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85 -Scoring:TransitionGroupPicker:PeakPickerMRM:peak_width $param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width
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86 #end if
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87 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise:
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88 -Scoring:TransitionGroupPicker:PeakPickerMRM:signal_to_noise $param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise
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89 #end if
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90 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
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91 -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
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92 #end if
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93 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
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94 -Scoring:TransitionGroupPicker:PeakPickerMRM:method
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95 #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
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96 "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
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97 #else
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98 $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
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99 #end if
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100 #end if
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101 #if $param_Scoring_DIAScoring_dia_extraction_window:
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102 -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
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103 #end if
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104 #if $param_Scoring_DIAScoring_dia_centroided:
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105 -Scoring:DIAScoring:dia_centroided
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106 #end if
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107 #if $param_Scoring_DIAScoring_dia_byseries_intensity_min:
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108 -Scoring:DIAScoring:dia_byseries_intensity_min $param_Scoring_DIAScoring_dia_byseries_intensity_min
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109 #end if
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110 #if $param_Scoring_DIAScoring_dia_byseries_ppm_diff:
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111 -Scoring:DIAScoring:dia_byseries_ppm_diff $param_Scoring_DIAScoring_dia_byseries_ppm_diff
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112 #end if
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113 #if $param_Scoring_DIAScoring_dia_nr_isotopes:
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114 -Scoring:DIAScoring:dia_nr_isotopes $param_Scoring_DIAScoring_dia_nr_isotopes
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115 #end if
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116 #if $param_Scoring_DIAScoring_dia_nr_charges:
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117 -Scoring:DIAScoring:dia_nr_charges $param_Scoring_DIAScoring_dia_nr_charges
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118 #end if
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119 #if $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff:
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120 -Scoring:DIAScoring:peak_before_mono_max_ppm_diff $param_Scoring_DIAScoring_peak_before_mono_max_ppm_diff
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121 #end if
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122 #if $param_Scoring_EMGScoring_max_iteration:
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123 -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
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124 #end if
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125 #if $param_Scoring_EMGScoring_deltaRelError:
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126 -Scoring:EMGScoring:deltaRelError $param_Scoring_EMGScoring_deltaRelError
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127 #end if
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128 #if $adv_opts.adv_opts_selector=='advanced':
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129 #if $adv_opts.param_rt_norm:
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130 -rt_norm $adv_opts.param_rt_norm
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131 #end if
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132 #if $adv_opts.param_swath_windows_file:
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133 -swath_windows_file $adv_opts.param_swath_windows_file
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134 #end if
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135 #if $adv_opts.param_sort_swath_maps:
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136 -sort_swath_maps
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137 #end if
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138 #if $adv_opts.param_use_ms1_traces:
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139 -use_ms1_traces
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140 #end if
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141 #if $adv_opts.param_min_upper_edge_dist:
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142 -min_upper_edge_dist $adv_opts.param_min_upper_edge_dist
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143 #end if
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144 #if $adv_opts.param_extra_rt_extraction_window:
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145 -extra_rt_extraction_window $adv_opts.param_extra_rt_extraction_window
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146 #end if
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147 #if $adv_opts.param_min_rsq:
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148 -min_rsq $adv_opts.param_min_rsq
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149 #end if
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150 #if $adv_opts.param_min_coverage:
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151 -min_coverage $adv_opts.param_min_coverage
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152 #end if
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153 #if $adv_opts.param_split_file_input:
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154 -split_file_input
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155 #end if
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156 #if $adv_opts.param_use_elution_model_score:
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157 -use_elution_model_score
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158 #end if
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159 #if $adv_opts.param_readOptions:
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160 -readOptions
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161 #if " " in str($adv_opts.param_readOptions):
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162 "$adv_opts.param_readOptions"
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163 #else
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164 $adv_opts.param_readOptions
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165 #end if
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166 #end if
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167 #if $adv_opts.param_tempDirectory:
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168 -tempDirectory "$adv_opts.param_tempDirectory"
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169 #end if
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170 #if $adv_opts.param_extraction_function:
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171 -extraction_function
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172 #if " " in str($adv_opts.param_extraction_function):
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173 "$adv_opts.param_extraction_function"
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174 #else
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175 $adv_opts.param_extraction_function
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176 #end if
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177 #end if
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178 #if $adv_opts.param_batchSize:
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179 -batchSize $adv_opts.param_batchSize
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180 #end if
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181 #if $adv_opts.param_force:
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182 -force
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183 #end if
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184 #if $adv_opts.param_Scoring_quantification_cutoff:
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185 -Scoring:quantification_cutoff $adv_opts.param_Scoring_quantification_cutoff
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186 #end if
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187 #if $adv_opts.param_Scoring_write_convex_hull:
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188 -Scoring:write_convex_hull
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189 #end if
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190 #if $adv_opts.param_Scoring_Scores_use_shape_score:
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191 -Scoring:Scores:use_shape_score
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192 #end if
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193 #if $adv_opts.param_Scoring_Scores_use_coelution_score:
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194 -Scoring:Scores:use_coelution_score
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195 #end if
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196 #if $adv_opts.param_Scoring_Scores_use_rt_score:
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197 -Scoring:Scores:use_rt_score
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198 #end if
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199 #if $adv_opts.param_Scoring_Scores_use_library_score:
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200 -Scoring:Scores:use_library_score
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201 #end if
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202 #if $adv_opts.param_Scoring_Scores_use_intensity_score:
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203 -Scoring:Scores:use_intensity_score
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204 #end if
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205 #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
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206 -Scoring:Scores:use_nr_peaks_score
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207 #end if
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208 #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
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209 -Scoring:Scores:use_total_xic_score
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210 #end if
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211 #if $adv_opts.param_Scoring_Scores_use_sn_score:
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212 -Scoring:Scores:use_sn_score
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213 #end if
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214 #if $adv_opts.param_Scoring_Scores_use_dia_scores:
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215 -Scoring:Scores:use_dia_scores
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216 #end if
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217 #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
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218 -Scoring:Scores:use_ms1_correlation
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219 #end if
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220 #if $adv_opts.param_Scoring_Scores_use_ms1_fullscan:
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221 -Scoring:Scores:use_ms1_fullscan
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222 #end if
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223 #end if
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224 </command>
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225 <inputs>
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226 <param name="param_in" type="data" format="mzxml,mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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227 <sanitizer>
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228 <valid initial="string.printable">
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229 <remove value="'"/>
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230 <remove value="""/>
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231 </valid>
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232 </sanitizer>
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233 </param>
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234 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML','tsv' or 'csv')" help="(-tr) "/>
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235 <param name="param_tr_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" help="(-tr_type) ">
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236 <option value="traML">traML</option>
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237 <option value="tsv">tsv</option>
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238 <option value="csv">csv</option>
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239 </param>
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240 <param name="param_tr_irt" type="data" format="traml" optional="True" label="transition file ('TraML')" help="(-tr_irt) "/>
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241 <param name="output_fmt" type="select" label="Select feature list output format">
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242 <option value="featurexml">FeatureXML</option>
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243 <option value="tsv">TSV output file (mProphet compatible)</option>
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244 </param>
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245 <param name="param_rt_extraction_window" type="float" value="600.0" label="Only extract RT around this value (-1 means extract over the whole range, a value of 600 means to extract around +/- 300 s of the expected elution)" help="(-rt_extraction_window) "/>
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246 <param name="param_mz_extraction_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window used (in Thomson, to use ppm see -ppm flag)" help="(-mz_extraction_window) "/>
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247 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
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248 <param name="param_Scoring_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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249 <param name="param_Scoring_rt_normalization_factor" type="float" value="100.0" 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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250 <param name="param_Scoring_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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251 <param name="param_Scoring_TransitionGroupPicker_min_peak_width" type="float" value="14.0" label="Minimal peak width (s), discard all peaks below this value (-1 means no action)" help="(-min_peak_width) "/>
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252 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks" type="text" size="30" value="true" 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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253 <sanitizer>
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254 <valid initial="string.printable">
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255 <remove value="'"/>
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256 <remove value="""/>
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257 </valid>
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258 </sanitizer>
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259 </param>
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260 <param name="param_Scoring_TransitionGroupPicker_recalculate_peaks_max_z" type="float" value="0.75" 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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261 <param name="param_Scoring_TransitionGroupPicker_minimal_quality" type="float" value="-1.5" 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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262 <param name="param_Scoring_TransitionGroupPicker_compute_peak_quality" type="text" size="30" value="true" 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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263 <sanitizer>
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264 <valid initial="string.printable">
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265 <remove value="'"/>
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266 <remove value="""/>
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267 </valid>
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268 </sanitizer>
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269 </param>
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270 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_sgolay_frame_length" type="integer" value="11" 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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271 <param name="param_Scoring_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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272 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_gauss_width" type="float" value="30.0" label="Gaussian width in seconds, estimated peak size" help="(-gauss_width) "/>
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273 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_use_gauss" type="text" size="30" value="false" label="Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)" help="(-use_gauss) ">
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274 <sanitizer>
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275 <valid initial="string.printable">
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276 <remove value="'"/>
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277 <remove value="""/>
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278 </valid>
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279 </sanitizer>
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280 </param>
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281 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_peak_width" type="float" value="-1.0" 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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282 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_signal_to_noise" type="float" min="0.0" optional="True" value="0.1" 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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283 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" type="boolean" truevalue="-Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks" falsevalue="" checked="true" optional="True" label="Try to remove overlapping peaks during peak picking" help="(-remove_overlapping_peaks) "/>
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284 <param name="param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" type="select" optional="True" value="corrected" label="Which method to choose for chromatographic peak-picking (OpenSWATH legacy, corrected picking or Crawdad)" help="(-method) ">
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285 <option value="legacy">legacy</option>
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286 <option value="corrected">corrected</option>
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287 <option value="crawdad">crawdad</option>
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288 </param>
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289 <param name="param_Scoring_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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290 <param name="param_Scoring_DIAScoring_dia_centroided" type="boolean" truevalue="-Scoring:DIAScoring:dia_centroided" falsevalue="" checked="false" optional="True" label="Use centroded DIA data" help="(-dia_centroided) "/>
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291 <param name="param_Scoring_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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292 <param name="param_Scoring_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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293 <param name="param_Scoring_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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294 <param name="param_Scoring_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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295 <param name="param_Scoring_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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296 <param name="param_Scoring_EMGScoring_max_iteration" type="integer" value="10" label="Maximum number of iterations using by Levenberg-Marquardt algorithm" help="(-max_iteration) "/>
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297 <param name="param_Scoring_EMGScoring_deltaRelError" type="float" value="0.1" label="" help="(-deltaRelError) "/>
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298 <expand macro="advanced_options">
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299 <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) If set, tr_irt may be omitted"/>
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300 <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
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301 <param name="param_sort_swath_maps" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
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302 <param name="param_use_ms1_traces" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
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303 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
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304 <param name="param_extra_rt_extraction_window" type="float" min="0.0" optional="True" value="0.0" label="Output an XIC with a RT-window that by this much larger (" help="(-extra_rt_extraction_window) e.g. to visually inspect a larger area of the chromatogram)"/>
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305 <param name="param_min_rsq" type="float" value="0.95" label="Minimum r-squared of RT peptides regression" help="(-min_rsq) "/>
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306 <param name="param_min_coverage" type="float" value="0.6" label="Minimum relative amount of RT peptides to keep" help="(-min_coverage) "/>
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307 <param name="param_split_file_input" type="boolean" truevalue="-split_file_input" falsevalue="" checked="false" optional="True" label="The input files each contain one single SWATH (alternatively: all SWATH are in separate files)" help="(-split_file_input) "/>
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308 <param name="param_use_elution_model_score" type="boolean" truevalue="-use_elution_model_score" falsevalue="" checked="false" optional="True" label="Turn on elution model score (EMG fit to peak)" help="(-use_elution_model_score) "/>
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309 <param name="param_readOptions" type="select" optional="True" value="normal" label="Whether to run OpenSWATH directly on the input data, cache data to disk first or to perform a datareduction step first" help="(-readOptions) If you choose cache, make sure to also set tempDirectory">
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310 <option value="normal">normal</option>
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311 <option value="cache">cache</option>
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312 </param>
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313 <param name="param_tempDirectory" type="text" size="30" value="/tmp/" label="Temporary directory to store cached files for example" help="(-tempDirectory) ">
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314 <sanitizer>
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315 <valid initial="string.printable">
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316 <remove value="'"/>
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317 <remove value="""/>
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318 </valid>
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319 </sanitizer>
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320 </param>
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321 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
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322 <option value="tophat">tophat</option>
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323 <option value="bartlett">bartlett</option>
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324 </param>
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325 <param name="param_batchSize" type="integer" min="0" optional="True" value="0" label="The batch size of chromatograms to process (0 means to only have one batch, sensible values are around 500-1000)" help="(-batchSize) "/>
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326 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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327 <param name="param_Scoring_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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328 <param name="param_Scoring_write_convex_hull" type="boolean" truevalue="-Scoring: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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329 <param name="param_Scoring_Scores_use_shape_score" type="boolean" truevalue="-Scoring: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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330 <param name="param_Scoring_Scores_use_coelution_score" type="boolean" truevalue="-Scoring: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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331 <param name="param_Scoring_Scores_use_rt_score" type="boolean" truevalue="-Scoring: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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332 <param name="param_Scoring_Scores_use_library_score" type="boolean" truevalue="-Scoring:Scores:use_library_score" falsevalue="" checked="true" optional="True" label="Use the library score" help="(-use_library_score) "/>
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333 <param name="param_Scoring_Scores_use_intensity_score" type="boolean" truevalue="-Scoring:Scores:use_intensity_score" falsevalue="" checked="true" optional="True" label="Use the intensity score" help="(-use_intensity_score) "/>
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334 <param name="param_Scoring_Scores_use_nr_peaks_score" type="boolean" truevalue="-Scoring: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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335 <param name="param_Scoring_Scores_use_total_xic_score" type="boolean" truevalue="-Scoring: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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336 <param name="param_Scoring_Scores_use_sn_score" type="boolean" truevalue="-Scoring: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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337 <param name="param_Scoring_Scores_use_dia_scores" type="boolean" truevalue="-Scoring:Scores:use_dia_scores" falsevalue="" checked="true" optional="True" label="Use the DIA (SWATH) scores" help="(-use_dia_scores) "/>
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338 <param name="param_Scoring_Scores_use_ms1_correlation" type="boolean" truevalue="-Scoring: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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339 <param name="param_Scoring_Scores_use_ms1_fullscan" type="boolean" truevalue="-Scoring: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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340 </expand>
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341 </inputs>
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342 <outputs>
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4
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343 <data name="out_features" format="featurexml">
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344 <filter>output_fmt == 'featurexml'</filter>
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345 </data>
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346 <data name="out_tsv" format="tabular">
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347 <filter>output_fmt == 'tsv'</filter>
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348 </data>
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0
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349 <data name="param_out_chrom" format="mzml"/>
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350 </outputs>
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351 <help>**What it does**
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352
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353 Complete workflow to run OpenSWATH
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354
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355
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356 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_OpenSwathWorkflow.html</help>
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357 <expand macro="references"/>
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358 </tool>
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