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1 <tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
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2
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3 <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
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4
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5 <requirements>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="binary">Rscript</requirement>
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8 <requirement type="package" version="1.44.0">xcms</requirement>
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9 <requirement type="package" version="2.1">xcms_w4m_script</requirement>
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10 </requirements>
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11
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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15
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16 <command>
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17 xcms.r
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18 #if $inputs.input == "lib":
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19 library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
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20 #elif $inputs.input == "zip_file":
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21 zipfile $inputs.zip_file
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22 #end if
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23
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24 xfunction xcmsSet
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25 ## profmethod $profmethod
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26 nSlaves \${GALAXY_SLOTS:-1} method $methods.method
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27 #if $methods.method == "centWave":
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28 ppm $methods.ppm
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29 peakwidth "c($methods.peakwidth)"
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30 #if $methods.options_scanrange.option == "show":
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31 scanrange "c($methods.options_scanrange.scanrange)"
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32 #end if
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33 #if $methods.options_c.option == "show":
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34 mzdiff $methods.options_c.mzdiff
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35 snthresh $methods.options_c.snthresh
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36 integrate $methods.options_c.integrate
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37 noise $methods.options_c.noise
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38 prefilter "c($methods.options_c.prefilter)"
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39 #end if
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40 #elif $methods.method == "matchedFilter":
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41 step $methods.step
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42 fwhm $methods.fwhm
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43 #if $methods.options_m.option == "show":
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44 ## sigma "$methods.options_m.sigma"
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45 max $methods.options_m.max
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46 snthresh $methods.options_m.snthresh
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47 ## mzdiff $methods.options_m.mzdiff
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48 steps $methods.options_m.steps
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49 ## sleep $methods.options_m.sleep
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50 #end if
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51 #elif $methods.method == "MSW":
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52 snthr $methods.snthr
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53 nearbyPeak $methods.nearbyPeak
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54 winSize.noise $methods.winSize_noise
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55 amp.Th $methods.amp_Th
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56 scales "c($methods.scales)"
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57 SNR.method "$methods.SNR_method"
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58 #end if
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59 && (mv xcmsSet.RData $xsetRData;
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60 mv sampleMetadata.tsv $sampleMetadata;
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61 mv TICs_raw.pdf $ticsRawPdf;
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62 mv BPCs_raw.pdf $bpcsRawPdf;
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63 mv xset.log $log);
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64 cat $log
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65 </command>
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66
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67 <inputs>
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68
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69 <conditional name="inputs">
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70 <param name="input" type="select" label="Choose your inputs method" >
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71 <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option>
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72 <option value="lib" >Library directory name</option>
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73 </param>
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74 <when value="zip_file">
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75 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
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76 </when>
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77 <when value="lib">
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78 <param name="library" type="text" size="40" label="Library directory name" help="The name of your directory containing all your data" >
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79 <validator type="empty_field"/>
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80 </param>
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81 </when>
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82
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83 </conditional>
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84
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85
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86 <!--
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87 <param name="profmethod" type="select" label="Method to use for profile generation (profmethod)" >
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88 <option value="bin" selected="true">bin</option>
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89 <option value="binlin">binlin</option>
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90 <option value="binlinbase">binlinbase</option>
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91 <option value="intlin">intlin</option>
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92 </param>
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93 <param name="nSlaves" type="integer" value="9" label="MPI-slaves CPU" help="number of MPI-slaves to use for parallel peak detection" />
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94 -->
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95 <conditional name="methods">
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96 <param name="method" type="select" label="Extraction method for peaks detection" help="[method] See the help section below">
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97 <option value="centWave" >centWave</option>
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98 <option value="matchedFilter" selected="true">matchedFilter</option>
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99 <option value="MSW">MSW</option>
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100 </param>
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101
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102 <!-- centWave Filter options -->
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103 <when value="centWave">
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104 <param name="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="[ppm]" />
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105 <param name="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="[peakwidth]" />
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106 <conditional name="options_scanrange">
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107 <param name="option" type="select" label="Scan range option " >
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108 <option value="show">show</option>
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109 <option value="hide" selected="true">hide</option>
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110 </param>
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111 <when value="show">
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112 <param name="scanrange" type="text" value="" label="scanrange" help="scan range to process, for example (16,365)" >
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113 <validator type="empty_field"/>
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114 </param>
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115 </when>
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116 </conditional>
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117
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118 <conditional name="options_c">
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119 <param name="option" type="select" label="Advanced options" >
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120 <option value="show">show</option>
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121 <option value="hide" selected="true">hide</option>
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122 </param>
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123 <when value="show">
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124 <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" />
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125 <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " />
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126 <param name="integrate" type="select" label="peak limits method" help="[integrate]" >
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127 <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option>
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128 <option value="2">peak limits based on real data (more sensitive to noise)</option>
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129 </param>
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130 <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
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131 <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
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132 </when>
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133 </conditional>
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134 </when>
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135
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136 <!-- matched Filter options -->
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137 <when value="matchedFilter">
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138 <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" />
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139 <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" />
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140 <conditional name="options_m">
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141 <param name="option" type="select" label="Advanced options" >
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142 <option value="show">show</option>
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143 <option value="hide" selected="true">hide</option>
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144 </param>
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145 <when value="show">
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146 <!--
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147 <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" />
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148 -->
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149 <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" />
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150 <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" />
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151 <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" />
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152 <!--
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153 <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
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154 -->
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155 </when>
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156 </conditional>
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157 </when>
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158
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159 <!-- MSW Filter options -->
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160 <when value="MSW">
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161 <param name="nearbyPeak" type="select" label="Determine whether to include the nearby small peaks of major peaks" help="[nearbyPeak]" >
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162 <option value="TRUE">TRUE</option>
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163 <option value="FALSE">FALSE</option>
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164 </param>
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165 <param name="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />
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166 <param name="snthr" type="integer" value="3" label="SNR (Signal to Noise Ratio) threshold" help="[snthr]" />
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167 <param name="amp_Th" type="float" value="0.002" label="Minimum required relative amplitude of the peak" help="[amp.Th] Ratio to the maximum of CWT coefficients" />
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168 <param name="scales" type="text" value="seq(1,22,3)" label="Scales for the Continuous Wavelet Transform (CWT)" help="[scales] Scales are linked to the width of the peaks that are to be detected. Tape as indicaded seq('n,n,n') or c(n,n) : seq(from, to, by steps), c - linear vector " />
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169 <param name="SNR_method" type="text" value="data.mean" label="SNR (Signal to Noise Ratio) method" help="[SNR.method] Method to estimate noise level. Currently, only 95 percentage quantile is supported." />
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170 </when>
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171 </conditional>
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172 </inputs>
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173
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174 <outputs>
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175 <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
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176 <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
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177 <data name="ticsRawPdf" format="pdf" label="xset.TICs_raw.pdf" />
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178 <data name="bpcsRawPdf" format="pdf" label="xset.BPCs_raw.pdf" />
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179 <data name="log" format="txt" label="xset.log.txt" />
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180 </outputs>
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181
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182 <tests>
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183 <test>
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184 <param name="inputs.input" value="zip_file" />
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185 <param name="inputs.zip_file" value="sacuri.zip" />
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186 <param name="methods.method" value="matchedFilter" />
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187 <param name="methods.step" value="0.01" />
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188 <param name="methods.fwhm" value="4" />
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189 <param name="methods.options_m.option" value="show" />
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190 <param name="methods.options_m.max" value="50" />
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191 <param name="methods.options_m.snthresh" value="1" />
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192 <param name="methods.options_m.steps" value="2" />
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193 <output name="xsetRData" file="xset.RData" />
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194 <output name="sampleMetadata" file="sampleMetadata.tsv" />
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195 <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
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196 <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
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197 <output name="log" file="xset.log.txt" />
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198 </test>
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199 </tests>
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200
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201 <help>
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202
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203 .. class:: infomark
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204
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205 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
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206
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207 .. class:: infomark
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208
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209 **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
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210
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211 | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
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212
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213 ---------------------------------------------------
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214
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215 ============
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216 Xcms.xcmsSet
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217 ============
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218
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219 -----------
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220 Description
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221 -----------
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222
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223 This tool is used for preprocessing analyte data from multiple LC/MS files (formats NetCDF, mzXML and mzData). It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
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224 You can read a tutorial on how to perform xcms preprocessing which is available here_.
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225
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226 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
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227
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228
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229 -----------------
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230 Workflow position
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231 -----------------
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232
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233 **Upstream tools**
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234
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235 ========================= ================= ======= =========
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236 Name output file format parameter
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237 ========================= ================= ======= =========
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238 NA NA zip NA
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239 ========================= ================= ======= =========
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240
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241
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242 **Downstream tools**
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243
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244 +---------------------------+--------------------+-----------------+
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245 | Name | Output file | Format |
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246 +===========================+====================+=================+
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247 |xcms.group | xset.RData | rdata.xcms.raw |
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248 +---------------------------+--------------------+-----------------+
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249 |PCA ellipsoid by factors | sampleMetadata.tsv | Tabular |
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250 +---------------------------+--------------------+-----------------+
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251 |Anova | sampleMetadata.tsv | Tabular |
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252 +---------------------------+--------------------+-----------------+
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253
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254
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255 **Example of a metabolomic workflow**
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256
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257 .. image:: XCMS_Galaxy_workflow.png
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258
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259
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260 ------
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261
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262 .. class:: infomark
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263
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264 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
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265
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266 ---------------------------------------------------
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267
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268
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269
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270 -----------
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271 Input files
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272 -----------
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273
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274 +---------------------------+------------+
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275 | Parameter : num + label | Format |
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276 +===========================+============+
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277 | 1 : Choose your inputs | zip |
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278 +---------------------------+------------+
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279
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280 **Choose your inputs**
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281
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282 You have two methods for your inputs:
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283
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284 | Zip file (recommended): You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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285 | library folder: You must specify the name of your "library" (folder) created within your space project (for example: /projet/externe/institut/login/galaxylibrary/yourlibrary). Your library must contain all your conditions as sub-directories.
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286
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287 ----------
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288 Parameters
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289 ----------
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290
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291 Extraction method for peaks detection
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292 -------------------------------------
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293
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294 **Matched Filter**
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295
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296 | One parameter to consider is the Gaussian model peak width used for matched filtration,an integral part of the peak detection algorithm.
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297 | For a discussion of how model peak width affects the signal to noise ratio, see Danielsson et al. (2002).
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298
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299
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300 **cent Wave**
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301
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302 | This algorithm is most suitable for high resolution LC/{TOF,OrbiTrap,FTICR}-MS data in centroid mode.
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303 | Due to the fact that peak centroids are used, a binning step is not necessary.
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304 | The method is capable of detecting close-by-peaks and also overlapping peaks. Some efforts are made to detect the exact peak boundaries to get precise peak integrals.
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305
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306 **MSW**
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307
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308 | Wavelet based, used for direct infusion data. Continuous wavelet transform (CWT) can be used to locate chromatographic peaks on different scales.
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309 | If you wish to have more details about the other parameters, you can read the following documents:
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310 | -Example of preprocessing data with XCMS : http://www.bioconductor.org/packages/2.12/bioc/vignettes/xcms/inst/doc/xcmsPreprocess.pdf
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311 | -Details and explanations for all the parameters of XCMS package: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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312
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313
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314 ------------
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315 Output files
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316 ------------
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317
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318 xset.TICs_raw.pdf
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319
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320 | "Total Ion Chromatograms" graph in pdf format.
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321
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322 xset.BPCs_raw.pdf
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323
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324 | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
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325
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326 sampleMetadata.tsv
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327
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328 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
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329 | This file is necessary in the Anova and PCA step of the workflow.
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330
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331 xset.RData: rdata.xcms.raw format
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332
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333 | Rdata file that is necessary in the second step of the workflow "xcms.group".
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334
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335 ------
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336
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337 .. class:: infomark
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338
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339 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
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340
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341 ---------------------------------------------------
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342
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343 ---------------
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344 Working example
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345 ---------------
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346
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347 Input files
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348 -----------
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349
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350 | zip_file -> **sacuri.zip**
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351
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352 Parameters
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353 ----------
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354
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355 | Method -> **matchedFilter**
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356 | step -> **0.01**
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357 | fwhm -> **4**
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358 | Advanced option -> **show**
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359 | max: -> **50**
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360 | snthresh -> **1**
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361 | steps -> **2**
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362
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363
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364 Output files
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365 ------------
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366
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367 | **1) xset.RData: RData file**
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368
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369 | **2) Example of a sampleMetadata.tsv :**
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370
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371
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372 +---------------------------+------------+---------+
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373 | sampleMetadata | class | polarity|
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374 +===========================+============+=========+
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375 |HU_neg_017 | bio |negative |
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376 +---------------------------+------------+---------+
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377 |HU_neg_028 | bio |negative |
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378 +---------------------------+------------+---------+
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379 |HU_neg_034 | bio |negative |
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380 +---------------------------+------------+---------+
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381 |Blanc04 | blank |negative |
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382 +---------------------------+------------+---------+
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383 |Blanc06 | blank |negative |
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384 +---------------------------+------------+---------+
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385 |Blanc09 | blank |negative |
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386 +---------------------------+------------+---------+
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387
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388
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389
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390 | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**
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391
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392 .. image:: xcms_tics.png
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393
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394
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395 </help>
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396
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397
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398 <citations>
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399 <citation type="doi">10.1021/ac051437y</citation>
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400 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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401 </citations>
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402
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403 </tool>
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