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1 <tool id="openms_peak_list_preprocessor" version="0.1" name="Peak List Preprocessor">
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2 <description>
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3 Wizard to apply multiple OpenMS signal preprocessing tools for peak lists.
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4 </description>
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5 <macros>
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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="requires" />
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10 <configfiles>
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11 <configfile name="setup_input">cp '$input' 'output.mzML'</configfile>
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12 <configfile name="rename">mv 'output.mzML' 'input.mzML'</configfile>
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13 <configfile name="copy_output">mv 'output.mzML' '$output'</configfile>
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14 <configfile name="resampler_config">[simple_options]
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15 #if $resample.do
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16 in=input.mzML
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17 out=output.mzML
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18 sampling_rate=$resample.sampling_rate
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19 #end if
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20 </configfile>
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21 <configfile name="noise_filter_config">[simple_options]
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22 #set $noise_filter_type = str($noise.type)
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23 in=input.mzML
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24 out=output.mzML
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25 #if $noise_filter_type == 'NoiseFilterGaussian'
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26
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27 #end if
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28 #if $noise_filter_type == 'NoiseFilterSGolay'
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29
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30 #end if
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31 </configfile>
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32 <configfile name="baseline_config">[simple_options]
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33 in=input.mzML
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34 out=output.mzML
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35 #if $baseline.do
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36
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37 #end if
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38 </configfile>
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39 <configfile name="peak_picker_config">[simple_options]
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40 #set $peak_picker_type = str($peak_picker.type)
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41 in=input.mzML
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42 out=output.mzML
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43 #if $peak_picker_type == 'PeakPickerHiRes'
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44 algorithm!signal_to_noise=$peak_picker.signal_to_noise
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45 algorithm!ms1_only=$peak_picker.ms1_only
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46 #end if
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47 #if $peak_picker_type == 'PeakPickerWavelet'
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48 algorithm!signal_to_noise=$peak_picker.signal_to_noise
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49 #if $peak_picker.peak_width.estimate
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50 algorithm!estimate_peak_width=true
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51 #else
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52 algorithm!estimate_peak_width=false
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53 algorithm!peak_width=$peak_picker.peak_width.peak_width
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54 #end if
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55 #end if
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56 </configfile>
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57 <configfile name="mass_corrector_config">[simple_options]
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58 in=input.mzML
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59 out=output.mzML
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60 </configfile>
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61 <configfile name="spectra_filter_config">[simple_options]
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62 in=input.mzML
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63 out=output.mzML
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64 #set $spectra_filter_type = str($spectra_filter.type)
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65 </configfile>
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66 </configfiles>
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67 <command interpreter="python">
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68 openms_wrapper.py
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69 --executable '__SHELL__' --config $setup_input
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70 #if $resample.do
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71 --executable '__SHELL__' --config $rename
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72 --executable 'Resampler' --config $resampler_config
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73 #end if
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74 #set $noise_filter_type = str($noise.type)
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75 #if $noise_filter_type != "none"
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76 --executable '__SHELL__' --config $rename
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77 --executable '$noise_filter_type' --config $noise_filter_config
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78 #end if
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79 #if $baseline.do
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80 --executable '__SHELL__' --config $rename
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81 --executable 'BaselineFilter' --config $baseline_config
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82 #end if
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83 #set $peak_picker_type = str($peak_picker.type)
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84 #if $peak_picker_type != "none"
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85 --executable '__SHELL__' --config $rename
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86 --executable '$peak_picker_type' --config $peak_picker_config
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87 #if $peak_picker_type == "PeakPickerHiRes"
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88 #if $peak_picker.use_high_res_mass_corrector
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89 --executable '__SHELL__' --config $rename
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90 --executable 'HighResPrecursorMassCorrector' --config $mass_corrector_config
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91 #end if
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92 #end if
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93 #end if
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94 #set $spectra_filter_type = str($spectra_filter.type)
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95 #if $spectra_filter_type != "none"
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96 --executable '__SHELL__' --config $rename
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97 --executable '$spectra_filter_type' --config $spectra_filter_config
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98 #end if
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99 --executable '__SHELL__' --config $copy_output
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100 </command>
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101 <inputs>
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102 <!-- TODO: Maybe even have a conversion step here. -->
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103 <param format="mzML" name="input" type="data" label="Input Peak List (mzML)"/>
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104 <conditional name="resample">
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105 <param name="do" type="boolean" label="Resample" help="If you want to use the Savitzky Golay filter, or Baseline filter with non equally spaced profile data, e.g. TOF data, you have should generate equally spaced data by resampling.">
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106 </param>
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107 <when value="false">
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108 </when>
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109 <when value="true">
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110 <expand macro="sampling_rate_param" />
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111 </when>
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112 </conditional>
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113 <conditional name="noise">
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114 <param name="type" type="select" label="Noise Filter" help="">
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115 <option value="none" select="true">None</option>
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116 <option value="NoiseFilterGaussian">Gaussian</option>
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117 <option value="NoiseFilterSGolay">Savitzky Golay</option>
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118 </param>
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119 <when value="none">
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120 </when>
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121 <when value="NoiseFilterGaussian">
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122 </when>
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123 <when value="NoiseFilterSGolay">
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124 </when>
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125 </conditional>
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126 <conditional name="baseline">
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127 <param name="do" type="boolean" label="Apply Baseline Filter" help="Executes the top-hat filter to remove the baseline of an MS experiment." />
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128 <when value="false">
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129 </when>
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130 <when value="true">
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131 </when>
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132 </conditional>
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133 <conditional name="peak_picker">
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134 <param name="type" type="select" label="Peak Picker" help="">
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135 <option value="none" select="true">None</option>
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136 <option value="PeakPickerHiRes">High Resolution</option>
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137 <option value="PeakPickerWavelet">Wavelet</option>
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138 </param>
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139 <when value="none">
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140 </when>
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141 <when value="PeakPickerHiRes">
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142 <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked. (0.0 disables SNT estimation!)" value="1.0" type="float" />
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143 <param name="ms1_only" type="boolean" label="MS1 Only" truevalue="true" falsevalue="false" />
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144 <param name="use_high_res_mass_corrector" label="Correct precursor m/z on centroided high resolution data." checked="false" type="boolean" />
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145 </when>
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146 <when value="PeakPickerWavelet">
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147 <param name="signal_to_noise" label="Signal-to-noise Ratio" help="Minimal signal to noise ratio for a peak to be picked." value="1.0" type="float" />
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148 <conditional name="peak_width">
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149 <param name="estimate" label="Estimate Peak Width" type="boolean" checked="false" />
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150 <when value="true">
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151 </when>
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152 <when value="false">
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153 <param name="peak_width" type="float" value="0.15" help="Approximate fwhm of the peaks." label="Peak Width" />
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154 </when>
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155 </conditional>
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156 </when>
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157 </conditional>
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158 <conditional name="spectra_filter">
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159 <param name="type" type="select" label="Apply Spectra Filter" help="">
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160 <option value="none" select="true">None</option>
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161 <option value="SpectraFilterNLargest">N Largest</option>
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162 <option value="SpectraFilterNormalizer">Normalizer</option>
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163 <option value="SpectraFilterScaler">Scaler</option>
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164 <option value="SpectraFilterBernNorm">Bern et. al. normalization</option>
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165 <option value="SpectraFilterMarkerMower">Marker Mower</option>
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166 <option value="SpectraFilterParentPeakMower">Parent Peak Mower</option>
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167 <option value="SpectraFilterSqrtMower">Square Root Mower</option>
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168 <option value="SpectraFilterThresholdMower">Threshold Mower</option>
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169 <option value="SpectraFilterWindowMower">Window Mower</option>
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170 </param>
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171 <when value="none">
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172 </when>
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173 <when value="SpectraFilterNLargest">
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174 <!-- 1 param -->
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175 </when>
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176 <when value="SpectraFilterNormalizer">
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177 <!-- 1 param -->
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178 </when>
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179 <when value="SpectraFilterScaler">
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180 <!-- 3 params -->
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181 </when>
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182 <when value="SpectraFilterBernNorm">
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183 </when>
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184 <when value="SpectraFilterMarkerMower">
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185 </when>
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186 <when value="SpectraFilterParentPeakMower">
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187 <!-- Tons of params -->
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188 </when>
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189 <when value="SpectraFilterSqrtMower">
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190 </when>
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191 <when value="SpectraFilterThresholdMower">
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192 <!-- 1 param -->
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193 </when>
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194 <when value="SpectraFilterWindowMower">
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195 <!-- 2 params -->
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196 </when>
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197 </conditional>
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198 </inputs>
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199 <outputs>
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200 <data format="mzml" name="output" />
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201 </outputs>
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202 <help>
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203 **What it does**
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204
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205 **Citation**
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206
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207 For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
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208
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209 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
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210 </help>
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211 </tool>
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