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1 <tool id="metams_lcms_pick_and_group" name="METAMS-LC/MS Pick, Align and Group" version="0.0.4">
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2 <description> Runs metaMS process for LC/MS feature picking, aligning and grouping</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.1">R_bioc_metams</requirement>
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5 </requirements>
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6 <command interpreter="Rscript">
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7 metaMS_cmd_pick_and_group.r
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8 $data_files
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9 $customMetaMSsettings
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10 $outputFile
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11 $xsetOut
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12 $polarity
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13 $htmlReportFile
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14 $htmlReportFile.files_path
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15 $outputLog
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16 </command>
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17 <inputs>
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18 <param name="data_files" type="data" format="prims.fileset.zip" label="Data files (.zip file with CDF, mzML or mzXML files)" help=".zip file containing the CDF, mzML or mzXML files of the new measurements"/>
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19
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20 <param name="protocolName" type="text" size="30" label="protocolName" value="e.g. Synapt.QTOF.RP"
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21 help="Choose a name to give for the specific settings in the parameters below"/><!-- TODO - let user choose this -->
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22
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23 <param name="polarity" type="select" size="30" label="polarity"
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24 help="Which polarity mode was used for measuring of the ms sample">
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25 <option value="positive" selected="true">positive</option>
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26 <option value="negative" >negative</option>
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27 </param>
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28
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29
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30 <!-- ===========NB : if peak picking, alignment OR CAMERA settings have to be reused for runGC wrapper in the future, we can use Galaxy macro expansions here
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31 to avoid defining these parameters again in the runGC wrapper ========================= -->
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32 <conditional name="peakPicking">
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33 <param name="method" type="select" size="30" label="PEAK PICKING method ====================================================="
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34 help="matchedFilter=Feature detection in the chromatographic time domain ; centWave=Feature detection for high resolution LC/MS data">
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35 <option value="matchedFilter" selected="true">matchedFilter</option>
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36 <option value="centWave" >centWave</option>
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37 </param>
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38 <when value="matchedFilter">
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39 <param name="fwhm" type="integer" size="10" value="20" label="fwhm"
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40 help="full width at half maximum of matched filtration gaussian model peak. Only used to calculate the actual sigma" />
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41 <param name="sigma_denom" type="float" size="10" value="2.3548" label="sigma_denominator"
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42 help="denominator for standard deviation (width) of matched filtration model peak (e.g. sigma = fwhm/2.3548)" />
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43 <param name="max" type="integer" size="10" value="50" label="max"
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44 help="maximum number of peaks per extracted ion chromatogram" />
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45 <param name="snthresh" type="integer" size="10" value="4" label="snthresh"
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46 help="signal to noise ratio cutoff" />
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47 <param name="step" type="float" size="10" value="0.05" label="step"
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48 help="step size to use for profile generation"/>
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49 <param name="steps" type="integer" size="10" value="2" label="steps"
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50 help="number of steps to merge prior to filtration"/>
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51 <param name="mzdiff" type="float" size="10" value="0.8" label="mzdiff"
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52 help="minimum difference in m/z for peaks with overlapping retention times"/>
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53 </when>
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54 <when value="centWave">
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55 <param name="ppm" type="integer" size="10" value="25" label="ppm"
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56 help="maxmial tolerated m/z deviation in consecutive scans, in ppm" />
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57 <param name="peakwidth" type="text" size="10" value="20,50" label="peakwidth"
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58 help="Chromatographic peak width, given as range (min,max) in seconds" />
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59 <param name="snthresh" type="integer" size="10" value="10" label="snthresh"
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60 help="signal to noise ratio cutoff" />
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61 <param name="prefilter" type="text" size="10" value="3,100" label="prefilter=c(k,I)"
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62 help="Prefilter step for the first phase. Mass traces are only retained if
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63 they contain at least k peaks with intensity > = I" />
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64 <param name="mzCenterFun" type="select" size="30" label="mzCenterFun"
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65 help="Function to calculate the m/z center of the feature: wMean intensity weighted mean of the
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66 feature m/z values, mean mean of the feature m/z values, apex use m/z value at peak apex,
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67 wMeanApex3 intensity weighted mean of the m/z value at peak apex and the m/z value left and
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68 right of it, meanApex3 mean of the m/z value at peak apex and the m/z value left and right of it">
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69 <option value="wMean" selected="true">wMean</option>
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70 <option value="mean" >mean</option>
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71 <option value="apex" >apex</option>
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72 <option value="wMeanApex3" >wMeanApex3</option>
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73 <option value="meanApex3" >meanApex3</option>
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74 </param>
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75 <param name="integrate" type="select" size="30" label="integrate"
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76 help="Integration method. If =1 peak limits are found through descent
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77 on the mexican hat filtered data, if =2 the descent is done on the real data.
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78 Method 2 is very accurate but prone to noise, while method 1 is more robust to noise but less exact">
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79 <option value="1" selected="true">1</option>
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80 <option value="2" >2</option>
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81 </param>
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82 <param name="mzdiff" type="float" size="10" value="-0.001" label="mzdiff"
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83 help="minimum difference in m/z for peaks with overlapping retention times, can be negative to allow overlap" />
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84 <param name="fitgauss" type="integer" size="10" value="20" label="fitgauss"
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85 help="logical, if Yes: a Gaussian is fitted to each peak" >
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86 <option value="TRUE" selected="true">Yes</option>
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87 <option value="FALSE" >No</option>
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88 </param>
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89 <param name="noise" type="integer" size="10" value="0" label="noise"
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90 help="optional argument which is useful for data that was centroided without any intensity
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91 threshold, centroids with intensity < noise are omitted from ROI detection" />
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92 </when>
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93 </conditional>
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94
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95
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96 <param name="min_class_fraction" type="float" size="10" value="0.3" label="ALIGNMENT min.class.fraction ====================================================="
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97 help="Minimum fraction of samples necessary in the alignment to make it a valid alignment/group"/>
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98 <param name="min_class_size" type="integer" size="10" value="3" label="min.class.size"
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99 help="Minimum number of samples necessary in the alignment to make it a valid alignment/group. The lowest criteria
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100 between this and min.class.fraction will be used." />
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101 <param name="mzwid" type="float" size="10" value="0.1" label="mzwid"
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102 help="width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples"/>
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103 <param name="bws" type="text" size="10" value="30,10" label="bws"
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104 help="bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel
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105 to apply to the peak density chromatogram. Fill in two values separated by comma. First value is used for
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106 first grouping round, seccond value is used for last grouping/alignment round after retention time
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107 correction. "/>
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108
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109 <conditional name="retcor">
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110 <param name="retcormethod" type="select" size="30" label="retcormethod"
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111 help="retention time correction method. 'peakgroups' is the default density based approach, 'obiwarp' is
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112 alignment data by Ordered Bijective Interpolated Warping ">
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113 <option value="peakgroups" selected="true">peakgroups</option>
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114 <option value="obiwarp" >obiwarp</option>
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115 </param>
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116 <when value="peakgroups">
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117 <param name="retcorfamily" type="select" size="30" label="retcorfamily"
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118 help="retention time correction method type/family">
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119 <option value="symmetric" selected="true">symmetric</option>
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120 <option value="gaussian">gaussian</option>
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121 </param>
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122 <param name="smooth" type="select" size="30" label="smooth"
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123 help="either 'loess' for non-linear alignment or 'linear' for linear alignment">
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124 <option value="linear" selected="true">linear</option>
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125 <option value="loess">loess (TODO - waiting for metaMS to add/parse this option)</option>
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126 </param>
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127 <param name="missingratio" type="float" size="10" value="0.2" label="missingratio"
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128 help="ratio of missing samples to allow in retention time correction groups"/>
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129 <param name="extraratio" type="float" size="10" value="0.1" label="extraratio"
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130 help="ratio of extra peaks to allow in retention time correction correction groups"/>
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131 </when>
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132 <when value="obiwarp">
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133 <param name="profStep" type="integer" size="10" value="1" label="profStep"
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134 help="step size (in m/z) to use for profile generation from the raw data files" />
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135 </when>
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136 </conditional>
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137
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138 <param name="fillPeaks" type="select" size="30" label="fillPeaks"
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139 help="Fill missing peaks in peak groups/alignments that do not include peaks from every sample.
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140 This method produces intensity values for those missing samples by integrating raw data in peak group region.">
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141 <option value="TRUE" selected="true">Yes</option>
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142 <option value="FALSE">No</option>
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143 </param>
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144 <param name="perfwhm" type="float" size="10" value="0.6" label="CAMERA perfwhm ====================================================="
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145 help="percentage of FWHM width"/>
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146 <param name="cor_eic_th" type="float" size="10" value="0.7" label="cor_eic_th"
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147 help="correlation threshold (0..1)" />
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148 <param name="ppm" type="float" size="10" value="5.0" label="ppm"
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149 help="General ppm error" />
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150
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151 <param name="groupCorr_graphMethod" type="select" size="30" label="(groupCorr)graphMethod"
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152 help="Method selection for grouping peaks after correlation analysis into pseudospectra.">
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153 <option value="hcs" selected="true">hcs</option>
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154 </param>
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155
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156 <param name="groupCorr_pval" type="float" size="10" value="0.05" label="(groupCorr)pval"
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157 help="significant correlation threshold" />
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158
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159 <param name="groupCorr_calcCiS" type="select" size="30" label="(groupCorr)calcCiS"
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160 help="Use correlation inside samples for peak grouping">
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161 <option value="TRUE" selected="true">Yes</option>
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162 <option value="FALSE">No</option>
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163 </param>
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164
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165 <param name="groupCorr_calcIso" type="select" size="30" label="(groupCorr)calcIso"
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166 help="Use isotopic relationship for peak grouping">
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167 <option value="TRUE" >Yes</option>
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168 <option value="FALSE" selected="true">No</option>
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169 </param>
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170
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171 <param name="groupCorr_calcCaS" type="select" size="30" label="(groupCorr)calcCaS"
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172 help="Use correlation across samples for peak grouping">
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173 <option value="TRUE" >Yes</option>
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174 <option value="FALSE" selected="true">No</option>
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175 </param>
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176
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177
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178 <param name="findIsotopes_maxcharge" type="integer" size="10" value="3" label="(findIsotopes)maxcharge"
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179 help="max. ion charge" />
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180
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181 <param name="findIsotopes_maxiso" type="integer" size="10" value="4" label="(findIsotopes)maxiso"
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182 help="max. number of expected isotopes" />
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183
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184 <param name="findIsotopes_minfrac" type="float" size="10" value="0.5" label="(findIsotopes)minfrac"
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185 help="The ratio for the number of samples, which must satisfy the C12/C13 rule for isotope annotation" />
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186
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187
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188 <param name="findAdducts_multiplier" type="integer" size="10" value="3" label="(findAdducts)multiplier"
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189 help="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" />
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190
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191
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192
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193 </inputs>
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194 <configfiles>
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195
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196 <configfile name="customMetaMSsettings">## ====================================
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197 ## metaMS process settings
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198 customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}",
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199 chrom = "LC",
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200 PeakPicking = list(
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201 method = "${peakPicking.method}",
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202 #if $peakPicking.method == "matchedFilter"
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203 fwhm = ${peakPicking.fwhm},
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204 sigma = ${peakPicking.fwhm}/${peakPicking.sigma_denom},
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205 max = ${peakPicking.max},
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206 snthresh = ${peakPicking.snthresh},
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207 step = ${peakPicking.step},
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208 steps = ${peakPicking.steps},
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209 mzdiff = ${peakPicking.mzdiff}),
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210 #else
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211 ppm = ${peakPicking.ppm},
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212 peakwidth = c(${peakPicking.peakwidth}),
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213 snthresh = ${peakPicking.snthresh},
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214 prefilter = c(${peakPicking.prefilter}),
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215 mzCenterFun = "${peakPicking.mzCenterFun}",
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216 integrate = ${peakPicking.integrate},
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217 mzdiff = ${peakPicking.mzdiff},
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218 fitgauss = ${peakPicking.fitgauss},
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219 noise = ${peakPicking.noise}),
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220 #end if
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221 Alignment = list(
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222 min.class.fraction = ${min_class_fraction},
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223 min.class.size = ${min_class_size},
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224 mzwid = ${mzwid},
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225 bws = c(${bws}),
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226 retcormethod = "${retcor.retcormethod}",
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227 #if $retcor.retcormethod == "peakgroups"
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228 smooth = "${retcor.smooth}",
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229 missingratio = ${retcor.missingratio},
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230 extraratio = ${retcor.extraratio},
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231 retcorfamily = "${retcor.retcorfamily}",
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232 #else
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233 ##repeating the method as workaround/ backwards compatibility (can remove this one after fix from metaMS):
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234 method = "${retcor.retcormethod}",
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235 profStep = ${retcor.profStep},
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236 #end if
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237 fillPeaks = ${fillPeaks}),
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238 CAMERA = list(
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239 perfwhm = ${perfwhm},
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240 cor_eic_th = ${cor_eic_th},
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241 ppm= ${ppm},
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242 graphMethod= "${groupCorr_graphMethod}",
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243 pval= ${groupCorr_pval},
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244 calcCiS= ${groupCorr_calcCiS},
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245 calcIso= ${groupCorr_calcIso},
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246 calcCaS= ${groupCorr_calcCaS},
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247 maxcharge= ${findIsotopes_maxcharge},
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248 maxiso= ${findIsotopes_maxiso},
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249 minfrac= ${findIsotopes_minfrac},
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250 multiplier= ${findAdducts_multiplier}
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251 ))</configfile>
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252
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253 </configfiles>
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254
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255 <outputs>
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256 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - peaks table (TSV)"/>
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257 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
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258 <data name="xsetOut" format="rdata" label="${tool.name} on ${on_string} - xcmsSet (RDATA)"/>
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259 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - report (HTML)"/>
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260 </outputs>
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261 <tests>
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262 <test>
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263 </test>
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264 </tests>
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265 <help>
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266
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267 .. class:: infomark
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268
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269 Runs metaMS process for LC/MS feature feature picking, aligning and grouping.
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270 This part of the metaMS process makes use of the XCMS and CAMERA tools and algorithms.
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271 CAMERA is used for automatic deconvolution/annotation of LC/ESI-MS data.
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272 The figure below shows the main parts of the metaMS process wrapped by this tool.
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273
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274 .. image:: $PATH_TO_IMAGES/metaMS_pick_align_camera.png
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275
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276
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277 From CAMERA documentation:
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278
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279 .. image:: $PATH_TO_IMAGES/CAMERA_results.png
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280
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281 **References**
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282
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283 If you use this Galaxy tool in work leading to a scientific publication please
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284 cite the following papers:
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285
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286 Wehrens, R.; Weingart, G.; Mattivi, F. (2014).
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287 metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics.
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288 Journal of chromatography B: biomedical sciences and applications, 996 (1): 109-116.
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289 doi: 10.1016/j.jchromb.2014.02.051
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290 handle: http://hdl.handle.net/10449/24012
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291
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292 Wrapper by Pieter Lukasse.
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293
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294
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295 </help>
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296 <citations>
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297 <citation type="doi">10.1016/j.jchromb.2014.02.051</citation> <!-- example
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298 see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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299 -->
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300 </citations>
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301 </tool> |
