Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 34:6550698fe60f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 16:02:04 +0000
parents f5d51091cf84
children
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f5d51091cf84 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Chromatographic peak detection</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_xcms.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/xcms_xcmsSet.r
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14
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15 image '$image'
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17 BPPARAM \${GALAXY_SLOTS:-1}
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18
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19 #if $filterSection.filterAcquisitionNum != "":
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20 filterAcquisitionNum "c($filterSection.filterAcquisitionNum)"
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21 #end if
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22 #if $filterSection.filterRt != "":
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23 filterRt "c($filterSection.filterRt)"
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24 #end if
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25 #if $filterSection.filterMz != "":
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26 filterMz "c($filterSection.filterMz)"
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27 #end if
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29 method $methods.method
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31 #if $methods.method == "CentWave":
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32 @COMMAND_CENTWAVE@
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33 peaklist $methods.CentWaveAdv.peaklist
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34 ## List of regions-of-interest (ROI)
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35 #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI
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36 @COMMAND_CENTWAVEADVROI@
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37 #elif $methods.method == "CentWavePredIso":
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38 @COMMAND_CENTWAVE@
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39 ## List of regions-of-interest (ROI)
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40 #set $sectionROI = $methods.CentWaveAdvROI
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41 @COMMAND_CENTWAVEADVROI@
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42 snthreshIsoROIs $sectionROI.snthreshIsoROIs
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43 maxCharge $sectionROI.maxCharge
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44 maxIso $sectionROI.maxIso
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45 mzIntervalExtension $sectionROI.mzIntervalExtension
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46 polarity $sectionROI.polarity
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47 #elif $methods.method == "MatchedFilter":
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48 fwhm $methods.fwhm
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49 binSize $methods.binSize
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50 ## Advanced
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51 impute $methods.MatchedFilterAdv.impute_cond.impute
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52 #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase":
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53 #if $methods.MatchedFilterAdv.impute_cond.baseValue != "":
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54 baseValue $methods.MatchedFilterAdv.impute_cond.baseValue
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55 #end if
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56 distance $methods.MatchedFilterAdv.impute_cond.distance
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57 #end if
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58 #if $methods.MatchedFilterAdv.sigma != "":
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59 sigma $methods.MatchedFilterAdv.sigma
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60 #end if
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61 max $methods.MatchedFilterAdv.max
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62 snthresh $methods.MatchedFilterAdv.snthresh
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63 steps $methods.MatchedFilterAdv.steps
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64 mzdiff $methods.MatchedFilterAdv.mzdiff
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65 peaklist $methods.MatchedFilterAdv.peaklist
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66 #elif $methods.method == "MSW":
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67 snthresh $methods.snthresh
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68 verboseColumns $methods.verboseColumns
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69 scales "c($methods.scales)"
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70 nearbyPeak $methods.nearbyPeak
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71 ampTh $methods.ampTh
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72 #end if
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73
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74 @COMMAND_FILE_LOAD@
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75
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76 @COMMAND_LOG_EXIT@
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77 ]]></command>
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78
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79 <inputs>
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80
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81 <param name="image" type="data" format="rdata.msnbase.raw,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from MSnbase readMSData" />
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82
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83 <section name="filterSection" title="Spectra Filters" expanded="False">
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84 <param argument="filterAcquisitionNum" type="text" value="" optional="true" label="Filter on Acquisition Numbers" help="min,max">
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85 <expand macro="input_validator_range_integer"/>
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86 </param>
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87 <param argument="filterRt" type="text" value="" optional="true" label="Filter on Retention Time" help="min,max">
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88 <expand macro="input_validator_range_integer"/>
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89 </param>
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90 <param argument="filterMz" type="text" value="" optional="true" label="Filter on Mz" help="min,max">
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91 <expand macro="input_validator_range_integer"/>
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92 </param>
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93 </section>
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94
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95 <conditional name="methods">
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96 <param name="method" type="select" label="Extraction method for peaks detection" help="See the help section below">
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97 <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
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98 <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
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99 <option value="CentWavePredIso">CentWaveWithPredIsoROIs - performs a two-step centWave-based chromatographic peak detection</option>
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100 <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
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101 </param>
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102
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103 <!-- CentWave -->
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104 <when value="CentWave">
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105 <expand macro="input_centwave"/>
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106 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
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107 <expand macro="input_centwaveAdv"/>
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108 <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." />
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109 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False">
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110 <expand macro="input_centwaveAdvROI" optional="true"/>
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111 </section>
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112 </section>
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113 </when>
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114
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115 <!-- MatchedFilter -->
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116 <when value="MatchedFilter">
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117 <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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118 <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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119 <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
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120 <conditional name="impute_cond">
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121 <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
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122 <option value="none">none - no linear interpolation</option>
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123 <option value="lin">lin - linear interpolation</option>
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124 <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
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125 <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
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126 </param>
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127 <when value="none" />
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128 <when value="lin" />
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129 <when value="linbase">
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130 <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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131 <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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132 </when>
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133 <when value="intlin" />
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134 </conditional>
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135 <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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136 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
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137 <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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138 <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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139 <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-binSize*steps " />
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140 <param argument="peaklist" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Get a list of found chromatographic peaks" help="Generates a tabular file with all the chromatographic peaks obtained." />
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141 <!-- index -->
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142 </section>
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143 </when>
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144
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145 <!-- CentWaveWithPredIsoROIs -->
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146 <when value="CentWavePredIso">
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147 <expand macro="input_centwave"/>
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148 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
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149 <expand macro="input_centwaveAdv"/>
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150 </section>
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151 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="True">
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152 <expand macro="input_centwaveAdvROI" optional="true" />
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153 <param argument="snthreshIsoROIs" type="float" value="6.25" label="Signal to noise ratio cutoff" help="used in the second centWave run to identify peaks for predicted isotope ROIs." />
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154 <param argument="maxCharge" type="integer" value="3" label="Maximal isotope charge" help="Isotopes will be defined for charges ‘1:maxCharge’." />
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155 <param argument="maxIso" type="integer" value="5" label="Number of isotope peaks that should be predicted for each peak identified in the first centWave run" />
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156 <param argument="mzIntervalExtension" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is the mz range for the predicted isotope ROIs should be extended to increase detection of low intensity peaks" />
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157 <param argument="polarity" type="select" label="Polarity of the data">
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158 <option value="unknown">unknown</option>
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159 <option value="positive">positive</option>
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160 <option value="negative">negative</option>
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161 </param>
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162 </section>
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163 </when>
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164
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165 <!-- MSW -->
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166 <when value="MSW">
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167 <!---@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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168 <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
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169 <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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170 <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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171 <expand macro="input_validator_list_integer"/>
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172 </param>
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173 <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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174 <!-- peakScaleRange -->
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175 <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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176 <!-- minNoiseLevel -->
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177 <!-- ridgeLength -->
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178 <!-- peakThr -->
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179 <!-- tuneIn -->
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180 <!---@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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181 </when>
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182 </conditional>
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183
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184 <expand macro="input_file_load"/>
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185 </inputs>
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186
0
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187 <outputs>
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188 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
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189 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
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190 <data name="peaklist_out" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
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191 <filter>methods['method'] in ['CentWave', 'MatchedFilter'] and (methods['CentWaveAdv']['peaklist'])</filter>
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192 </data>
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193 </outputs>
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194
0
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195 <tests>
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196
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197 <!--<test>
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198 <param name="image" value="faahKO.raw.Rdata" ftype="rdata" />
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199 <section name="filterSection">
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200 <param name="filterAcquisitionNum" value="100,5000" />
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201 <param name="filterRt" value="3000,4000" />
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202 <param name="filterMz" value="300,400" />
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203 </section>
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204 <conditional name="methods">
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205 <param name="method" value="CentWave" />
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206 <param name="ppm" value="25" />
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207 <param name="peakwidth" value="20,50" />-->
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208 <!-- DISABLE: just for testing the arguments
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209 <section name="CentWaveAdv">
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210 <section name="CentWaveAdvROI">
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211 <param name="roiList" value="roiList.txt" ftype="tabular" />
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212 </section>
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213 </section>-->
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214 <!--</conditional>
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215 <expand macro="test_file_load_zip"/>
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216 <assert_stdout>
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217 <has_text text="ppm: 25" />
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218 <has_text text="peakwidth: 20, 50" />
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219 <has_text text="object with 4 samples" />
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220 <has_text text="Time range: 3006.9-3978.7 seconds (50.1-66.3 minutes)" />
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221 <has_text text="Mass range: 300-400 m/z" />
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222 <has_text text="Peaks: 1311 (about 328 per sample)" />
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223 <has_text text="Peak Groups: 0" />
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224 <has_text text="Sample classes: KO, WT" />
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225 </assert_stdout>
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226 </test>-->
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227 <test expect_num_outputs="2">
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228 <param name="image" value="ko15-raw.RData" ftype="rdata" />
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229 <conditional name="methods">
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230 <param name="method" value="CentWave" />
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231 <param name="ppm" value="25" />
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232 <param name="peakwidth" value="20,50" />
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233 </conditional>
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234 <expand macro="test_file_load_single_file" filename="ko15"/>
15
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235 <assert_stdout>
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236 <has_text text="ppm: 25" />
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237 <has_text text="peakwidth: 20, 50" />
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238 <has_text text="object with 1 samples" />
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239 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
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240 <has_text text="Mass range: 200.2-600 m/z" />
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241 <has_text text="Peaks: 2262 (about 2262 per sample)" />
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242 <has_text text="Peak Groups: 0" />
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243 <has_text text="Sample classes: ." />
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244 </assert_stdout>
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245 <!--<output name="xsetRData" file="ko15-xset.RData" />-->
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246 </test>
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247 <!-- DISABLE FOR TRAVIS
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248 Useful to generate test-data for the further steps
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249 <test>
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250 <param name="image" value="ko16-raw.RData" ftype="rdata" />
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251 <conditional name="methods">
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252 <param name="method" value="CentWave" />
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253 <param name="ppm" value="25" />
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254 <param name="peakwidth" value="20,50" />
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255 </conditional>
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256 <expand macro="test_file_load_single_file" filename="ko16"/>
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257 <assert_stdout>
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258 <has_text text="object with 1 samples" />
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259 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
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260 <has_text text="Mass range: 200.1-600 m/z" />
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261 <has_text text="Peaks: 2408 (about 2408 per sample)" />
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262 <has_text text="Peak Groups: 0" />
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263 <has_text text="Sample classes: ." />
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264 </assert_stdout>
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265 <output name="xsetRData" file="ko16-xset.RData" />
7
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266 </test>
6
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267 <test>
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268 <param name="image" value="wt15-raw.RData" ftype="rdata" />
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269 <conditional name="methods">
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270 <param name="method" value="CentWave" />
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271 <param name="ppm" value="25" />
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272 <param name="peakwidth" value="20,50" />
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273 </conditional>
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274 <expand macro="test_file_load_single_file" filename="wt15"/>
15
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275 <assert_stdout>
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276 <has_text text="object with 1 samples" />
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277 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
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278 <has_text text="Mass range: 200.2-599.8 m/z" />
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279 <has_text text="Peaks: 2278 (about 2278 per sample)" />
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280 <has_text text="Peak Groups: 0" />
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281 <has_text text="Sample classes: ." />
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282 </assert_stdout>
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283 <output name="xsetRData" file="wt15-xset.RData" />
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284 </test>
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285 <test>
15
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286 <param name="image" value="wt16-raw.RData" ftype="rdata" />
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287 <conditional name="methods">
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288 <param name="method" value="CentWave" />
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289 <param name="ppm" value="25" />
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290 <param name="peakwidth" value="20,50" />
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291 </conditional>
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292 <expand macro="test_file_load_single_file" filename="wt16"/>
15
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293 <assert_stdout>
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294 <has_text text="object with 1 samples" />
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295 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
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296 <has_text text="Mass range: 200.3-600 m/z" />
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lecorguille
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297 <has_text text="Peaks: 2303 (about 2303 per sample)" />
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298 <has_text text="Peak Groups: 0" />
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299 <has_text text="Sample classes: ." />
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300 </assert_stdout>
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301 <output name="xsetRData" file="wt16-xset.RData" />
15
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302 </test>
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303 -->
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304 <!-- DISABLE FOR TRAVIS
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305 Test to test the different methods parameters
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306 <test>
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307 <param name="image" value="ko15-raw.RData" ftype="rdata" />
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308 <conditional name="methods">
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309 <param name="method" value="MatchedFilter" />
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310 <param name="fwhm" value="35" />
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311 <section name="MatchedFilterAdv"
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312 <conditional name="impute_cond">
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313 <param name="impute" value="linbase" />
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314 <param name="baseValue" value="0.1" />
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315 <param name="distance" value="1" />
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316 </conditional>
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317 </section>
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318 </conditional>
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319 <assert_stdout>
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320 <has_text text="fwhm: 35" />
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321 <has_text text="impute: linbase" />
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322 <has_text text="baseValue: 0.1" />
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323 <has_text text="distance: 1" />
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324 </assert_stdout>
12
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325 </test>
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326 <test>
15
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327 <param name="image" value="ko15-raw.RData" ftype="rdata" />
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328 <conditional name="methods">
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329 <param name="method" value="CentWavePredIso" />
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330 <param name="ppm" value="56" />
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331 <param name="peakwidth" value="5.275,13.5" />
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332 <section name="CentWaveAdvROI">
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333 <param name="roiList" value="roiList.txt" ftype="tabular" />
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334 </section>
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335 </conditional>
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336 <assert_stdout>
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337 <has_text text=" scmin scmax mzmin mzmax length intensity" />
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338 <has_text text="1 200 300 300 350 100 5000" />
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339 </assert_stdout>
12
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340 </test>
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341 <test>
15
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342 <param name="image" value="ko15-raw.RData" ftype="rdata" />
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343 <conditional name="methods">
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344 <param name="method" value="MSW" />
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345 <param name="snthresh" value="4" />
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346 <param name="verboseColumns" value="true" />
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347 </conditional>
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348 <assert_stdout>
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349 <has_text text="snthresh: 4" />
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350 <has_text text="verboseColumns: TRUE" />
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351 </assert_stdout>
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352 </test>
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353 -->
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354 <!-- DISABLE FOR TRAVIS
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355 No more test-data/sacuri_dir_root.zip
12
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356 <test>
15
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357 <param name="image" value="sacuri_dir_root.zip" ftype="zip" />
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358 <conditional name="methods">
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359 <param name="method" value="MatchedFilter" />
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360 <param name="step" value="0.01" />
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361 <param name="fwhm" value="4" />
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362 <conditional name="options_m">
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363 <param name="option" value="show" />
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364 <param name="max" value="50" />
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365 <param name="snthresh" value="1" />
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366 <param name="steps" value="2" />
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367 </conditional>
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368 </conditional>
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369 <assert_stdout>
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370 <has_text text="object with 4 samples" />
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371 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
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372 <has_text text="Mass range: 50.0021-999.9863 m/z" />
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373 <has_text text="Peaks: 59359 (about 14840 per sample)" />
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374 <has_text text="Peak Groups: 0" />
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375 <has_text text="Sample classes: bio, blank" />
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376 </assert_stdout>
12
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377 </test>
15
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378 -->
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379 <!-- DISABLE FOR TRAVIS
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380 No more test-data/sacuri_current_root.zip
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381 <test>
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382 <param name="image" value="sacuri_current_root.zip" ftype="zip" />
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383 <conditional name="methods">
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384 <param name="method" value="CentWave" />
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385 <param name="ppm" value="25" />
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386 <param name="peakwidth" value="20,50" />
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387 </conditional>
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388 <assert_stdout>
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389 <has_text text="object with 4 samples" />
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390 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
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391 <has_text text="Mass range: 57.9756-593.4086 m/z" />
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392 <has_text text="Peaks: 1535 (about 384 per sample)" />
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393 <has_text text="Peak Groups: 0" />
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394 <has_text text="Sample classes: bio, blank" />
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395 </assert_stdout>
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396 </test>
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397 -->
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398 </tests>
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399
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400 <help><![CDATA[
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401
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402 @HELP_AUTHORS@
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403
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404 ===================
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405 xcms findChromPeaks
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406 ===================
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407
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408 -----------
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409 Description
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410 -----------
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411
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412 This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package.
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413 It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated.
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414 A tutorial on how to perform xcms preprocessing is available as GTN_ (Galaxy Training Network).
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415
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416 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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417 .. _GTN: https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms/tutorial.html
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418
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419
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420 -----------------
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421 Workflow position
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422 -----------------
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423
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424 **Upstream tools**
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425
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426 ========================= ================= ==============================
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427 Name Output file Format
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428 ========================= ================= ==============================
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429 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
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430 ========================= ================= ==============================
0
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431
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432
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433 **Downstream tools**
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434
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435 ==================================== ======================== =========================
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436 Name Output file Format
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437 ==================================== ======================== =========================
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438 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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439 ------------------------------------ ------------------------ -------------------------
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440 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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441 ==================================== ======================== =========================
0
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442
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443
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444 **Example of a metabolomic workflow**
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445
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446 .. image:: xcms_xcmsset_workflow.png
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447
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448 ---------------------------------------------------
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449
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450 ----------
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451 Parameters
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452 ----------
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453
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454 Extraction method for peaks detection
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455 -------------------------------------
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456
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457 **MatchedFilter**
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458
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459 | 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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460 | See the MatchedFilter_manual_
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461
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462 **CentWave**
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463
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464 | 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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465 | Due to the fact that peak centroids are used, a binning step is not necessary.
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466 | 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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467 | See the CentWave_manual_
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468
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469 **CentWaveWithPredIsoROIs**
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470
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471 | This method performs a two-step centWave-based chromatographic peak detection: in a first centWave run peaks are identified for which then the location of their potential isotopes in the mz-retention time is predicted. A second centWave run is then performed on these regions of interest (ROIs). The final list of chromatographic peaks comprises all non-overlapping peaks from both centWave runs.
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472 | See the CentWaveWithPredIsoROIs_manual_
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473
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474 **MSW**
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475
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476 | 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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477 | See the MSW_manual_
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478
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479 .. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
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480 .. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
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481 .. _CentWaveWithPredIsoROIs_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.html#heading-2
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482 .. _MSW_manual: https://rdrr.io/bioc/xcms/man/findPeaks-MSW.html#heading-2
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483
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484 @HELP_XCMS_MANUAL@
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485
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486 ------------
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487 Output files
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488 ------------
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489
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490 xset.RData: rdata.xcms.findchrompeaks format
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491
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492 | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
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493 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
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494
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495 ---------------------------------------------------
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c5fa73f1703f Uploaded
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496
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497 Changelog/News
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498 --------------
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499
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500 @HELP_XCMS_NEWVERSION_31200@
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501
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502 **Version 3.6.1+galaxy1 - 22/04/2020**
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503
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504 - NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods.
31
eb15a3841da4 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 30
diff changeset
505
eb15a3841da4 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 30
diff changeset
506
30
14b1c52fae62 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 29
diff changeset
507 @HELP_XCMS_NEWVERSION_3610@
14b1c52fae62 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 29
diff changeset
508
27
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
509 **Version 3.4.4.1 - 30/04/2019**
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
510
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
511 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
3bd53dcfa438 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 22
diff changeset
512
30
14b1c52fae62 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 29
diff changeset
513 @HELP_XCMS_NEWVERSION_3440@
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
514
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
515 **Version 3.0.0.0 - 08/03/2018**
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
516
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
517 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
518
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
519 - CHANGE: xcms.findChromPeaks no longer read the raw data. You have to run MSnbase readMSData first.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
520
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
521 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
522
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
523 - NEW: new Filters for Spectra
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
524
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
525 - NEW: new methods: CentWaveWithPredIsoROIs
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
526
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
527 - UPDATE: since xcms 3.0.0, some options are no more available: scanrange (replace by filters), profmethod, MatchedFilter.step, MatchedFilter.sigma, MSW.winSize.noise, MSW.SNR.method
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
528
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
529 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
530
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
531 - IMPROVEMENT: the tool "should" be now more flexible in term of file naming: it "should" accept space and comma. But don't be too imaginative :)
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
532
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
533 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
534
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
535
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
536 **Version 2.1.1 - 29/11/2017**
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
537
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
538 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
539
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
540
12
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
541 **Version 2.1.0 - 22/02/2017**
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
542
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
543 - 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".
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
544
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
545 - 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
15646e937936 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
lecorguille
parents: 11
diff changeset
546
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
547
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
548 **Version 2.0.11 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
549
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
550 - BUGFIX: propose scanrange for all methods
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
551
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
552
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
553 **Version 2.0.10 - 22/12/2016**
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
554
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
555 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
556
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
557
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
558 **Version 2.0.9 - 06/07/2016**
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
559
11
91311aa08cdc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 10
diff changeset
560 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
10
69eb0fc05837 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 7
diff changeset
561
15
b62808a2a008 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
lecorguille
parents: 13
diff changeset
562
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
563 **Version 2.0.8 - 06/04/2016**
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
564
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
565 - TEST: refactoring to pass planemo test using conda dependencies
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
566
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
567
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
568 **Version 2.0.7 - 10/02/2016**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
569
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
570 - BUGFIX: better management of errors. Datasets remained green although the process failed
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
571
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
572 - 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
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
573
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
574 - BUGFIX/IMPROVEMENT: New step to check and delete bad characters in the XML: accented characters in the storage path of the mass spectrometer
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
575
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
576 - UPDATE: refactoring of internal management of inputs/outputs
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
577
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
578 - TEST: refactoring to feed the new report tool
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
579
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
580
13
c934dd5c49a9 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1
lecorguille
parents: 12
diff changeset
581 **Version 2.0.2 - 18/01/2016**
5
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
582
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
583 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
584
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
585
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
586 **Version 2.0.2 - 09/10/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
587
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
588 - 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.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
589
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
590
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
591 **Version 2.0.2 - 02/06/2015**
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
592
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
593 - 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.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
594
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
595 - 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.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
596
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
597 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
598
588b0a7ae4b0 planemo upload
lecorguille
parents: 4
diff changeset
599 ]]></help>
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
600
6
0888f7ef739a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 5
diff changeset
601 <expand macro="citation" />
0
054e4681667c planemo upload
lecorguille
parents:
diff changeset
602 </tool>