Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 51:44ab040fffa0 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
author workflow4metabolomics
date Mon, 15 Jul 2024 15:55:46 +0000
parents 1c63d9d402e6
children 3d01d97f7335
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51
44ab040fffa0 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
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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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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11
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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/xcms_xcmsSet.r
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15 image '$image'
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16
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17 BPPARAM \${GALAXY_SLOTS:-1}
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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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28
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29 method $methods.method
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30
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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
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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>
0
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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"/>
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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" />
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266 </test>
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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"/>
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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>
37
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286 <param name="image" value="wt16-raw.RData" ftype="rdata" />
32
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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>
48
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292 <expand macro="test_file_load_single_file" filename="wt16"/>
32
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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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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>
48
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301 <output name="xsetRData" file="wt16-xset.RData" />
32
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302 </test>
37
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303 -->
32
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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>
37
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307 <param name="image" value="ko15-raw.RData" ftype="rdata" />
32
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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" />
37
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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>
32
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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" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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324 </assert_stdout>
31
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325 </test>
17
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326 <test>
37
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327 <param name="image" value="ko15-raw.RData" ftype="rdata" />
35
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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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lecorguille
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338 <has_text text="1 200 300 300 350 100 5000" />
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339 </assert_stdout>
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340 </test>
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341 <test>
37
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342 <param name="image" value="ko15-raw.RData" ftype="rdata" />
32
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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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lecorguille
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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 -->
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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354 <!-- DISABLE FOR TRAVIS
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355 No more test-data/sacuri_dir_root.zip
17
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356 <test>
35
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357 <param name="image" value="sacuri_dir_root.zip" ftype="zip" />
32
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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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lecorguille
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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" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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365 <param name="snthresh" value="1" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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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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lecorguille
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370 <has_text text="object with 4 samples" />
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lecorguille
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371 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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372 <has_text text="Mass range: 50.0021-999.9863 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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373 <has_text text="Peaks: 59359 (about 14840 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
374 <has_text text="Peak Groups: 0" />
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lecorguille
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375 <has_text text="Sample classes: bio, blank" />
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376 </assert_stdout>
17
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377 </test>
32
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378 -->
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379 <!-- DISABLE FOR TRAVIS
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diff changeset
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 ========================= ================= ==============================
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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 ==================================== ======================== =========================
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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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496
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497 Changelog/News
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498 --------------
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499
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1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
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500 @HELP_XCMS_NEWVERSION_31200@
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lecorguille
parents: 40
diff changeset
501
49
d4a0eed3099d "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 48
diff changeset
502 **Version 3.6.1+galaxy1 - 22/04/2020**
d4a0eed3099d "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 48
diff changeset
503
50
1c63d9d402e6 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dcc90f9cf76e6980c0a7d9698c89fab826e7adae"
workflow4metabolomics
parents: 49
diff changeset
504 - NEW: possibility to get a tabular file with all the chromatographic peaks obtained with the CentWave and MatchedFilter methods.
49
d4a0eed3099d "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 48
diff changeset
505
d4a0eed3099d "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 42a0bcde81726702194f1b4ecd741d0545648d40"
workflow4metabolomics
parents: 48
diff changeset
506
48
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 47
diff changeset
507 @HELP_XCMS_NEWVERSION_3610@
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 47
diff changeset
508
45
6f9224f32a34 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 44
diff changeset
509 **Version 3.4.4.1 - 30/04/2019**
6f9224f32a34 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 44
diff changeset
510
6f9224f32a34 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 44
diff changeset
511 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
6f9224f32a34 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
lecorguille
parents: 44
diff changeset
512
48
b3a1e98a4cc8 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
workflow4metabolomics
parents: 47
diff changeset
513 @HELP_XCMS_NEWVERSION_3440@
35
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
514
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
515 **Version 3.0.0.0 - 08/03/2018**
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
516
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
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.
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
518
35
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
519 - CHANGE: xcms.findChromPeaks no longer read the raw data. You have to run MSnbase readMSData first.
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
520
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
521 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
522
35
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
523 - NEW: new Filters for Spectra
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
524
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
525 - NEW: new methods: CentWaveWithPredIsoROIs
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
526
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
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
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
528
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
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.
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
530
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
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 :)
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
532
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
533 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
534
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
535
31
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 30
diff changeset
536 **Version 2.1.1 - 29/11/2017**
29
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 28
diff changeset
537
31
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 30
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
29
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 28
diff changeset
539
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
540
26
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
lecorguille
parents: 25
diff changeset
541 **Version 2.1.0 - 22/02/2017**
17
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
542
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
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".
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
544
26
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
lecorguille
parents: 25
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
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
lecorguille
parents: 25
diff changeset
546
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
547
16
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
548 **Version 2.0.11 - 22/12/2016**
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
549
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
550 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
551
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
552
15
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
553 **Version 2.0.10 - 22/12/2016**
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
554
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
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
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
556
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
557
13
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
558 **Version 2.0.9 - 06/07/2016**
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
559
15
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
560 - UPGRADE: upgrade the xcms version from 1.44.0 to 1.46.0
13
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
561
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
562
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
563 **Version 2.0.8 - 06/04/2016**
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
564
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
565 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
566
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
567
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
568 **Version 2.0.7 - 10/02/2016**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
569
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
570 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
571
4509e9dd03e4 planemo upload
lecorguille
parents: 3
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
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
573
4509e9dd03e4 planemo upload
lecorguille
parents: 3
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
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
575
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
576 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
577
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
578 - TEST: refactoring to feed the new report tool
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
579
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
580
29
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 28
diff changeset
581 **Version 2.0.2 - 18/01/2016**
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
582
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
583 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
584
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
585
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
586 **Version 2.0.2 - 09/10/2015**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
587
4509e9dd03e4 planemo upload
lecorguille
parents: 3
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.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
589
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
590
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
591 **Version 2.0.2 - 02/06/2015**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
592
4509e9dd03e4 planemo upload
lecorguille
parents: 3
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.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
594
4509e9dd03e4 planemo upload
lecorguille
parents: 3
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.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
596
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
597 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
598
1
2f5b78be1dd6 Uploaded
lecorguille
parents: 0
diff changeset
599 ]]></help>
0
1bad16e5e4ae planemo upload
lecorguille
parents:
diff changeset
600
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
601 <expand macro="citation" />
0
1bad16e5e4ae planemo upload
lecorguille
parents:
diff changeset
602 </tool>