Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 33:c363b9f1caef draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
author lecorguille
date Mon, 05 Mar 2018 04:15:34 -0500
parents 2bf1cb023c94
children efd23113d5f4
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1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.0">
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2 <description>Chromatographic peak detection</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @COMMAND_XCMS_SCRIPT@/xcms_xcmsSet.r
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14 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
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15 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
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16 #else
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17 zipfile '$input'
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18 #end if
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20 BPPARAM \${GALAXY_SLOTS:-1}
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22 #if $filterSection.filterAcquisitionNum != "":
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23 filterAcquisitionNum "c($filterSection.filterAcquisitionNum)"
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24 #end if
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25 #if $filterSection.filterRt != "":
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26 filterRt "c($filterSection.filterRt)"
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27 #end if
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28 #if $filterSection.filterMz != "":
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29 filterMz "c($filterSection.filterMz)"
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30 #end if
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31
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32 method $methods.method
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33
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34 #if $methods.method == "CentWave":
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35 ppm $methods.ppm
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36 peakwidth "c($methods.peakwidth)"
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37 ## Advanced
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38 snthresh $methods.CentWaveAdv.snthresh
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39 prefilter "c($methods.CentWaveAdv.prefilter)"
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40 mzCenterFun $methods.CentWaveAdv.mzCenterFun
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41 integrate $methods.CentWaveAdv.integrate
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42 mzdiff $methods.CentWaveAdv.mzdiff
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43 fitgauss $methods.CentWaveAdv.fitgauss
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44 noise $methods.CentWaveAdv.noise
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45 verboseColumns $methods.CentWaveAdv.verboseColumns
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46 #elif $methods.method == "MatchedFilter":
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47 fwhm $methods.fwhm
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48 binSize $methods.binSize
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49 impute $methods.impute_cond.impute
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50 #if $methods.impute_cond.impute == "linbase":
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51 #if $methods.impute_cond.baseValue != "":
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52 baseValue $methods.impute_cond.baseValue
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53 #end if
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54 distance $methods.impute_cond.distance
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55 #end if
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56 ## Advanced
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57 #if $methods.MatchedFilterAdv.sigma != "":
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58 sigma $methods.MatchedFilterAdv.sigma
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59 #end if
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60 max $methods.MatchedFilterAdv.max
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61 snthresh $methods.MatchedFilterAdv.snthresh
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62 steps $methods.MatchedFilterAdv.steps
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63 mzdiff $methods.MatchedFilterAdv.mzdiff
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64 #elif $methods.method == "MSW":
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65 snthresh $methods.snthresh
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66 verboseColumns $methods.verboseColumns
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67 scales "c($methods.scales)"
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68 nearbyPeak $methods.nearbyPeak
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69 ampTh $methods.ampTh
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70 #end if
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71 @COMMAND_LOG_EXIT@
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72 ]]></command>
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73
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74 <inputs>
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75
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76 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
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77
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78 <section name="filterSection" title="Spectra Filters" expanded="False">
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79 <param argument="filterAcquisitionNum" type="text" value="" optional="true" label="Filter on Acquisition Numbers" help="min,max">
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80 <expand macro="input_validator_range_integer"/>
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81 </param>
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82 <param argument="filterRt" type="text" value="" optional="true" label="Filter on Retention Time" help="min,max">
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83 <expand macro="input_validator_range_integer"/>
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84 </param>
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85 <param argument="filterMz" type="text" value="" optional="true" label="Filter on Mz" help="min,max">
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86 <expand macro="input_validator_range_integer"/>
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87 </param>
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88 </section>
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89
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90 <conditional name="methods">
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91 <param name="method" type="select" label="Extraction method for peaks detection" help="See the help section below">
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92 <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
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93 <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
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94 <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
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95 </param>
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96
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97 <!-- centWave Filter options -->
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98 <when value="CentWave">
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99 <param argument="ppm" type="integer" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
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100 <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
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101 <expand macro="input_validator_range_float"/>
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102 </param>
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103
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104 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
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105 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
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106 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
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107 <expand macro="input_validator_range_integer"/>
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108 </param>
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109 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
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110 <option value="wMean">intensity weighted mean of the peak's m/z values</option>
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111 <option value="mean">mean of the peak's m/z values</option>
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112 <option value="apex">use the m/z value at the peak apex</option>
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113 <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
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114 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
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115 </param>
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116 <param argument="integrate" type="select" label="Integration method" >
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117 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
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118 <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
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119 </param>
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120 <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />
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121 <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />
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122 <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." />
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123 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
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124 <!-- roiList -->
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125 <!-- firstBaselineCheck -->
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126 <!-- roiScales -->
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127 </section>
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128 </when>
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129
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130 <!-- matched Filter options -->
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131 <when value="MatchedFilter">
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132 <param argument="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="Only used to calculate the actual sigma" />
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133 <param argument="binSize" type="float" value="0.1" label="Step size to use for profile generation" help="The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size. (Previously step)" />
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134 <conditional name="impute_cond">
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135 <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
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136 <option value="none">none - no linear interpolation</option>
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137 <option value="lin">lin - linear interpolation</option>
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138 <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
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139 <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
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140 </param>
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141 <when value="none" />
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142 <when value="lin" />
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143 <when value="linbase">
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144 <param argument="baseValue" type="float" value="" optional="true" label="The base value to which empty elements should be set" help="The default for the ‘baseValue’ is half of the smallest value in ‘x’ (‘NA’s being removed)." />
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145 <param argument="distance" type="integer" value="0" label="Number of non-empty neighboring element of an empty element that should be considered for linear interpolation." />
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146 </when>
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147 <when value="intlin" />
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148 </conditional>
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149 <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
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150 <param argument="sigma" type="float" value="" optional="true" label="Standard deviation (width) of matched filtration model peak" help="Leave it to empty to calculate it using fwhm by default at fwhm/2.3548" />
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151 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
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152 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" help="defining the signal to noise cutoff to be used in the chromatographic peak detection step" />
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153 <param argument="steps" type="integer" value="2" label="Number of bins to be merged before filtration" help="(i.e. the number of neighboring bins that will be joined to the slice in which filtration and peak detection will be performed)" />
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154 <param argument="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="By default: 0.8-step*steps " />
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155 <!-- index -->
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156 </section>
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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 <!---@TODO <param argument="winSize_noise" type="integer" value="500" label="The local window size to estimate the noise level" help="[winSize.noise]" />-->
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162 <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
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163 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
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164 <param argument="scales" type="text" value="1,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,36,40,44,48,52,56,60,64" label="Scales of the Continuous Wavelet Transform (CWT)" help="Scales are linked to the width of the peaks that are to be detected." >
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165 <expand macro="input_validator_list_integer"/>
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166 </param>
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167 <param argument="nearbyPeak" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Determine whether to include the nearby small peaks of major peaks" />
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168 <!-- peakScaleRange -->
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169 <param argument="ampTh" type="float" value="0.01" label="Minimum required relative amplitude of the peak" help="Ratio to the maximum of CWT coefficients" />
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170 <!-- minNoiseLevel -->
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171 <!-- ridgeLength -->
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172 <!-- peakThr -->
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173 <!-- tuneIn -->
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174 <!---@TODO <param argument="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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175 </when>
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176 </conditional>
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177 </inputs>
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178
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179 <outputs>
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180 <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
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181 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
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182 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
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183 </data>
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184 <data name="ticsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" from_work_dir="TICs.pdf" />
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185 <data name="bpcsRawPdf" format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" from_work_dir="BICs.pdf" />
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186 <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
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187 </outputs>
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188
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189 <tests>
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190
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191 <test>
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192 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
33
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193 <section name="filterSection">
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194 <param name="filterAcquisitionNum" value="100,5000" />
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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195 <param name="filterRt" value="3000,4000" />
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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196 <param name="filterMz" value="300,400" />
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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197 </section>
32
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198 <conditional name="methods">
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199 <param name="method" value="CentWave" />
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200 <param name="ppm" value="25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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201 <param name="peakwidth" value="20,50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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202 </conditional>
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203 <assert_stdout>
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204 <has_text text="ppm: 25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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205 <has_text text="peakwidth: 20, 50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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206 <has_text text="object with 4 samples" />
33
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lecorguille
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207 <has_text text="Time range: 3006.9-3978.7 seconds (50.1-66.3 minutes)" />
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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208 <has_text text="Mass range: 300-400 m/z" />
c363b9f1caef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f
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209 <has_text text="Peaks: 1311 (about 328 per sample)" />
32
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210 <has_text text="Peak Groups: 0" />
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211 <has_text text="Sample classes: KO, WT" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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212 </assert_stdout>
31
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213 </test>
6
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lecorguille
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214 <test>
32
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215 <param name="input" value="MM14.mzML" ftype="mzxml" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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216 <conditional name="methods">
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217 <param name="method" value="CentWave" />
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218 <param name="ppm" value="56" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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219 <param name="peakwidth" value="5.275,13.5" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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220 </conditional>
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221 <assert_stdout>
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lecorguille
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222 <has_text text="ppm: 56" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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223 <has_text text="peakwidth: 5.275, 13.5" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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224 <has_text text="object with 1 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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225 <has_text text="Time range: 271-307.3 seconds (4.5-5.1 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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226 <has_text text="Mass range: 117.0357-936.7059 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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227 <has_text text="Peaks: 222 (about 222 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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228 <has_text text="Peak Groups: 0" />
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lecorguille
parents: 31
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229 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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230 </assert_stdout>
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231 </test>
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232 <!-- DISABLE FOR TRAVIS
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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233 Useful to generate test-data for the further steps
10
00ef27ba8abd planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
234 <test>
31
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235 <param name="input" value="ko15.CDF" ftype="netcdf" />
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
236 <conditional name="methods">
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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237 <param name="method" value="CentWave" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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238 <param name="ppm" value="25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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239 <param name="peakwidth" value="20,50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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240 </conditional>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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241 <assert_stdout>
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242 <has_text text="object with 1 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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243 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
244 <has_text text="Mass range: 200.2-600 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
245 <has_text text="Peaks: 2262 (about 2262 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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246 <has_text text="Peak Groups: 0" />
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lecorguille
parents: 31
diff changeset
247 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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248 </assert_stdout>
31
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249 </test>
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lecorguille
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250 <test>
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
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251 <param name="input" value="ko16.CDF" ftype="netcdf" />
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
252 <conditional name="methods">
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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253 <param name="method" value="CentWave" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
254 <param name="ppm" value="25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
255 <param name="peakwidth" value="20,50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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256 </conditional>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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257 <assert_stdout>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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258 <has_text text="object with 1 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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259 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
260 <has_text text="Mass range: 200.1-600 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
261 <has_text text="Peaks: 2408 (about 2408 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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262 <has_text text="Peak Groups: 0" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
263 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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264 </assert_stdout>
31
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265 </test>
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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266 <test>
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lecorguille
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267 <param name="input" value="wt15.CDF" ftype="netcdf" />
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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268 <conditional name="methods">
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lecorguille
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269 <param name="method" value="CentWave" />
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lecorguille
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270 <param name="ppm" value="25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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271 <param name="peakwidth" value="20,50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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272 </conditional>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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273 <assert_stdout>
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lecorguille
parents: 31
diff changeset
274 <has_text text="object with 1 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
275 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
276 <has_text text="Mass range: 200.2-599.8 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
277 <has_text text="Peaks: 2278 (about 2278 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
278 <has_text text="Peak Groups: 0" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
279 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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280 </assert_stdout>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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281 </test>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
282 <test>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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283 <param name="input" value="wt16.CDF" ftype="netcdf" />
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284 <conditional name="methods">
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285 <param name="method" value="CentWave" />
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286 <param name="ppm" value="25" />
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287 <param name="peakwidth" value="20,50" />
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288 </conditional>
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289 <assert_stdout>
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290 <has_text text="object with 1 samples" />
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291 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
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292 <has_text text="Mass range: 200.3-600 m/z" />
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293 <has_text text="Peaks: 2303 (about 2303 per sample)" />
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294 <has_text text="Peak Groups: 0" />
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295 <has_text text="Sample classes: ." />
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296 </assert_stdout>
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297 </test>
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298 -->
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299 <!-- DISABLE FOR TRAVIS
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300 Test to test the different methods parameters
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301 <test>
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302 <param name="input" value="MM8.mzML" ftype="mzxml" />
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303 <conditional name="methods">
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304 <param name="method" value="MatchedFilter" />
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305 <param name="fwhm" value="35" />
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306 <conditional name="impute_cond">
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307 <param name="impute" value="linbase" />
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308 <param name="baseValue" value="0.1" />
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309 <param name="distance" value="1" />
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310 </conditional>
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311 </conditional>
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312 <assert_stdout>
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313 <has_text text="fwhm: 35" />
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314 <has_text text="impute: linbase" />
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315 <has_text text="baseValue: 0.1" />
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316 <has_text text="distance: 1" />
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317 </assert_stdout>
31
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318 </test>
17
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319 <test>
32
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320 <param name="input" value="MM8.mzML" ftype="mzxml" />
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321 <conditional name="methods">
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322 <param name="method" value="MSW" />
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323 <param name="snthresh" value="4" />
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324 <param name="verboseColumns" value="true" />
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325 </conditional>
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326 <assert_stdout>
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327 <has_text text="snthresh: 4" />
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328 <has_text text="verboseColumns: TRUE" />
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329 </assert_stdout>
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330 </test>
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331 -->
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332 <!-- DISABLE FOR TRAVIS
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333 No more test-data/sacuri_dir_root.zip
17
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334 <test>
32
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335 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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336 <conditional name="methods">
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337 <param name="method" value="MatchedFilter" />
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338 <param name="step" value="0.01" />
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339 <param name="fwhm" value="4" />
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340 <conditional name="options_m">
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341 <param name="option" value="show" />
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342 <param name="max" value="50" />
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343 <param name="snthresh" value="1" />
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344 <param name="steps" value="2" />
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345 </conditional>
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346 </conditional>
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347 <assert_stdout>
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348 <has_text text="object with 4 samples" />
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349 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
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350 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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351 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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352 <has_text text="Peak Groups: 0" />
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353 <has_text text="Sample classes: bio, blank" />
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354 </assert_stdout>
17
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355 </test>
32
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356 -->
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357 <!-- DISABLE FOR TRAVIS
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358 No more test-data/sacuri_current_root.zip
17
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359 <test>
32
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360 <param name="input" value="sacuri_current_root.zip" ftype="zip" />
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361 <conditional name="methods">
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362 <param name="method" value="CentWave" />
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363 <param name="ppm" value="25" />
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364 <param name="peakwidth" value="20,50" />
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365 </conditional>
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366 <assert_stdout>
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367 <has_text text="object with 4 samples" />
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368 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
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369 <has_text text="Mass range: 57.9756-593.4086 m/z" />
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lecorguille
parents: 31
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370 <has_text text="Peaks: 1535 (about 384 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
371 <has_text text="Peak Groups: 0" />
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lecorguille
parents: 31
diff changeset
372 <has_text text="Sample classes: bio, blank" />
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373 </assert_stdout>
17
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diff changeset
374 </test>
32
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375 -->
0
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diff changeset
376 </tests>
15
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parents: 13
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377
1
2f5b78be1dd6 Uploaded
lecorguille
parents: 0
diff changeset
378 <help><![CDATA[
0
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379
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380 @HELP_AUTHORS@
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381
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382 ===================
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383 xcms findChromPeaks
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384 ===================
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385
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386 -----------
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387 Description
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388 -----------
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389
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390 This tool is used for preprocessing data from multiple LC/MS files (formats NetCDF, mzXML and mzData) using the xcms_ R package. It extracts ion from each sample independently and using a statistic model, peaks are filtered and integrated.
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391 You can read a tutorial on how to perform xcms preprocessing which is available here_.
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392
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393 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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394 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
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395
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396
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397 -----------------
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398 Workflow position
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399 -----------------
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400
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401 **Upstream tools**
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402
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403 ========================= ================= ======= =========
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404 Name output file format parameter
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405 ========================= ================= ======= =========
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406 NA NA zip NA
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407 ========================= ================= ======= =========
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408
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409
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410 **Downstream tools**
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411
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412 +---------------------------+--------------------+-----------------+
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413 | Name | Output file | Format |
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414 +===========================+====================+=================+
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415 |xcms.group | xset.RData | rdata.xcms.raw |
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416 +---------------------------+--------------------+-----------------+
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417 |PCA ellipsoid by factors | sampleMetadata.tsv | Tabular |
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418 +---------------------------+--------------------+-----------------+
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419 |Anova | sampleMetadata.tsv | Tabular |
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420 +---------------------------+--------------------+-----------------+
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421
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422
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423 **Example of a metabolomic workflow**
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424
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425 .. image:: xcms_xcmsset_workflow.png
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426
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428 ------
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430 .. class:: infomark
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431
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432 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
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433
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434 ---------------------------------------------------
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435
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437
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438 -----------
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439 Input files
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440 -----------
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441
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442 +---------------------------+----------------------------------+
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443 | Parameter : num + label | Format |
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444 +===========================+==================================+
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445 | OR : Zip file | zip |
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446 +---------------------------+----------------------------------+
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447 | OR : Single file | mzXML, mzML, mzData, netCDF |
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448 +---------------------------+----------------------------------+
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449
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450 **Choose your inputs**
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451
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452 You have two methods for your inputs:
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453
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454 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
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455 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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456
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457 Zip file: Steps for creating the zip file
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458 -----------------------------------------
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459
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460 **Step1: Creating your directory and hierarchize the subdirectories**
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461
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462
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463 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip_ software, otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
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464
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465 .. _7Zip: http://www.7-zip.org/
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466
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467 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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468 arabidopsis/wild/01.raw
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469 arabidopsis/mutant/01.raw
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470
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471 **Step2: Creating a zip file**
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472
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473 Create your zip file (e.g.: arabidopsis.zip).
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474
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475 **Step 3 : Uploading it to our Galaxy server**
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476
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477 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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478
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479 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org.
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480
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481 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf
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482
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483 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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484
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485 Advices for converting your files for the XCMS input
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486 ----------------------------------------------------
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487
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488 We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
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489
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490 **We recommend you the following parameters:**
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491
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492 Use Filtering: **True**
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494 Use Peak Picking: **True**
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495
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496 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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497
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498 Use zlib: **64**
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499
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500 Binary Encoding: **64**
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502 m/z Encoding: **64**
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504 Intensity Encoding: **64**
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505
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506
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507 ----------
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508 Parameters
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509 ----------
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510
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511 Extraction method for peaks detection
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512 -------------------------------------
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513
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514 **CentWave**
0
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515
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516 | The centWave algorithm perform peak density and wavelet based chromatographic peak detection for high resolution LC/MS data in centroid mode [Tautenhahn 2008].
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517 | Due to the fact that peak centroids are used, a binning step is not necessary.
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518 | 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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519 | See the CentWave_manual_
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520
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521 **MatchedFilter**
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522
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523 | The _matchedFilter_ algorithm identifies peaks in the chromatographic time domain as described in [Smith 2006]. The intensity values are binned by cutting The LC/MS data into slices (bins) of a mass unit (‘binSize’ m/z) wide. Within each bin the maximal intensity is selected. The chromatographic peak detection is then performed in each bin by extending it based on the ‘steps’ parameter to generate slices comprising bins ‘current_bin - steps +1’ to ‘current_bin + steps - 1’. Each of these slices is then filtered with matched filtration using a second-derative Gaussian as the model peak shape. After filtration peaks are detected using a signal-to-ratio cut-off. For more details and illustrations see [Smith 2006].
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524 | See the MatchedFilter_manual_
0
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525
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526 **MSW**
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527
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528 | 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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529 | See the MSW_manual_
0
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530
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531 .. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
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532 .. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
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533 .. _MSW_manual: https://rdrr.io/bioc/xcms/man/findPeaks-MSW.html#heading-2
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534
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535 @HELP_XCMS_MANUAL@
0
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536
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537 ------------
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538 Output files
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539 ------------
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540
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541 xset.TICs_raw.pdf
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542
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543 | "Total Ion Chromatograms" graph in pdf format.
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544
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545 xset.BPCs_raw.pdf
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546
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547 | "Base Peak Chromatograms" graph in pdf format with each class samples opposed.
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548
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549 sampleMetadata.tsv
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550
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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551 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
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552 | This file is necessary in the Anova and PCA step of the workflow.
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553
0
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554 xset.RData: rdata.xcms.raw format
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555
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556 | Rdata file that is necessary in the second step of the workflow "xcms.group".
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557
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558 ------
0
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559
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560 .. class:: infomark
0
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561
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562 The output file is an xset.RData file. You can continue your analysis using it in **xcms.group** tool.
0
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563
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564 ---------------------------------------------------
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565
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566 ---------------
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567 Working example
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568 ---------------
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569
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570 Input files
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571 -----------
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572
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573 | zip_file -> **sacuri.zip**
0
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574
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575 Parameters
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576 ----------
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577
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578 | Method -> **matchedFilter**
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579 | step -> **0.01**
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580 | fwhm -> **4**
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581 | Advanced option -> **show**
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582 | max: -> **50**
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583 | snthresh -> **1**
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584 | steps -> **2**
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585
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586
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587 Output files
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588 ------------
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589
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590 | **1) xset.RData: RData file**
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591
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592 | **2) Example of a sampleMetadata.tsv :**
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593
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594
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595 +---------------------------+------------+---------+
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596 | sampleMetadata | class | polarity|
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597 +===========================+============+=========+
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598 |HU_neg_017 | bio |negative |
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599 +---------------------------+------------+---------+
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600 |HU_neg_028 | bio |negative |
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601 +---------------------------+------------+---------+
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602 |HU_neg_034 | bio |negative |
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603 +---------------------------+------------+---------+
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604 |Blanc04 | blank |negative |
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605 +---------------------------+------------+---------+
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606 |Blanc06 | blank |negative |
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607 +---------------------------+------------+---------+
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608 |Blanc09 | blank |negative |
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609 +---------------------------+------------+---------+
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610
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611
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612
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613 | **3) Example of xset.TICs_raw.pdf (Total Ion Chromatograms) :**
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614
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615 .. image:: xcms_tics.png
0
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616
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617
4
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618 ---------------------------------------------------
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619
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620 Changelog/News
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621 --------------
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622
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623 **Version 3.0.0.0 - 14/02/2018**
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624
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625 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
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626
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627 - NEW: a bunch of new options: Spectra Filters, CentWave.mzCenterFun, CentWave.fitgauss, CentWave.verboseColumns, MatchedFilter.sigma
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628
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629 - UPDATE: since xcms 3.0.0, some options are no more available: scanrange, profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method
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630
31
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diff changeset
631 **Version 2.1.1 - 29/11/2017**
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632
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e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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633 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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634
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626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
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635 **Version 2.1.0 - 22/02/2017**
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602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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636
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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637 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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638
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626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
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639 - BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
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640
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f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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641 **Version 2.0.11 - 22/12/2016**
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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642
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
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643 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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644
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645 **Version 2.0.10 - 22/12/2016**
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
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646
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
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647 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
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648
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68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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649 **Version 2.0.9 - 06/07/2016**
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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650
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1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
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651 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
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68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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652
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60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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653 **Version 2.0.8 - 06/04/2016**
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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654
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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655 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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656
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657 **Version 2.0.7 - 10/02/2016**
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658
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659 - BUGFIX: better management of errors. Datasets remained green although the process failed
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660
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661 - BUGFIX/IMPROVEMENT: New checking steps around the imported data in order to raise explicte error message before or after launch XCMS: checking of bad characters in the filenames, checking of the XML integrity and checking of duplicates which can appear in the sample names during the XCMS process because of bad characters
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662
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663 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
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664
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lecorguille
parents: 3
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665 - UPDATE: refactoring of internal management of inputs/outputs
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666
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667 - TEST: refactoring to feed the new report tool
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668
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5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
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669 **Version 2.0.2 - 18/01/2016**
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lecorguille
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670
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671 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
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672
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673 **Version 2.0.2 - 09/10/2015**
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674
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675 - BUGFIX: Some users reported a bug in xcms.xcmsSet. The preprocessing stops itself and doesn't import the whole dataset contained in the zip file without warning. But meanwhile, please check your samplemetadata dataset and the number of rows.
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676
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677 **Version 2.0.2 - 02/06/2015**
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678
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679 - NEW: The W4M workflows will now take as input a zip file to ease the transfer and to improve dataset exchange between tools and users. (See How_to_upload). The previous "Library directory name" is still available but we invite user to switch on the new zip system as soon as possible.
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680
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681 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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682
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parents: 3
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683 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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684
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2f5b78be1dd6 Uploaded
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parents: 0
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685 ]]></help>
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686
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687 <expand macro="citation" />
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688 </tool>