Mercurial > repos > lecorguille > xcms_xcmsset

annotate abims_xcms_xcmsSet.xml @ 45:6f9224f32a34 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 60ad498b7bd01542a69d6603160d36494c97077a
author lecorguille
date Tue, 30 Apr 2019 05:13:39 -0400
parents ceff49826bf2
children bea0471f41b9
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1 <tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@WRAPPER_VERSION@.1">
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2 <description>Chromatographic peak detection</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <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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12 <command><![CDATA[
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13 @COMMAND_RSCRIPT@/xcms_xcmsSet.r
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15 image '$image'
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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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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 ## List of regions-of-interest (ROI)
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34 #set $sectionROI = $methods.CentWaveAdv.CentWaveAdvROI
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35 @COMMAND_CENTWAVEADVROI@
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36 #elif $methods.method == "CentWavePredIso":
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37 @COMMAND_CENTWAVE@
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38 ## List of regions-of-interest (ROI)
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39 #set $sectionROI = $methods.CentWaveAdvROI
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40 @COMMAND_CENTWAVEADVROI@
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41 snthreshIsoROIs $sectionROI.snthreshIsoROIs
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42 maxCharge $sectionROI.maxCharge
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43 maxIso $sectionROI.maxIso
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44 mzIntervalExtension $sectionROI.mzIntervalExtension
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45 polarity $sectionROI.polarity
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46 #elif $methods.method == "MatchedFilter":
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47 fwhm $methods.fwhm
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48 binSize $methods.binSize
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49 ## Advanced
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50 impute $methods.MatchedFilterAdv.impute_cond.impute
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51 #if $methods.MatchedFilterAdv.impute_cond.impute == "linbase":
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52 #if $methods.MatchedFilterAdv.impute_cond.baseValue != "":
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53 baseValue $methods.MatchedFilterAdv.impute_cond.baseValue
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54 #end if
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55 distance $methods.MatchedFilterAdv.impute_cond.distance
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56 #end if
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57 #if $methods.MatchedFilterAdv.sigma != "":
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58 sigma $methods.MatchedFilterAdv.sigma
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59 #end if
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60 max $methods.MatchedFilterAdv.max
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61 snthresh $methods.MatchedFilterAdv.snthresh
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62 steps $methods.MatchedFilterAdv.steps
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63 mzdiff $methods.MatchedFilterAdv.mzdiff
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64 #elif $methods.method == "MSW":
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65 snthresh $methods.snthresh
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66 verboseColumns $methods.verboseColumns
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67 scales "c($methods.scales)"
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68 nearbyPeak $methods.nearbyPeak
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69 ampTh $methods.ampTh
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70 #end if
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72 @COMMAND_FILE_LOAD@
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73
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74 @COMMAND_LOG_EXIT@
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75 ]]></command>
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76
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77 <inputs>
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78
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79 <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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80
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81 <section name="filterSection" title="Spectra Filters" expanded="False">
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82 <param argument="filterAcquisitionNum" type="text" value="" optional="true" label="Filter on Acquisition Numbers" help="min,max">
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83 <expand macro="input_validator_range_integer"/>
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84 </param>
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85 <param argument="filterRt" type="text" value="" optional="true" label="Filter on Retention Time" help="min,max">
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86 <expand macro="input_validator_range_integer"/>
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87 </param>
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88 <param argument="filterMz" type="text" value="" optional="true" label="Filter on Mz" help="min,max">
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89 <expand macro="input_validator_range_integer"/>
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90 </param>
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91 </section>
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92
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93 <conditional name="methods">
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94 <param name="method" type="select" label="Extraction method for peaks detection" help="See the help section below">
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95 <option value="MatchedFilter" selected="true">MatchedFilter - peak detection in chromatographic space</option>
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96 <option value="CentWave">CentWave - chromatographic peak detection using the centWave method</option>
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97 <option value="CentWavePredIso">CentWaveWithPredIsoROIs - performs a two-step centWave-based chromatographic peak detection</option>
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98 <option value="MSW">MSW - single-spectrum non-chromatography MS data peak detection</option>
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99 </param>
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100
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101 <!-- CentWave -->
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102 <when value="CentWave">
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103 <expand macro="input_centwave"/>
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104 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
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105 <expand macro="input_centwaveAdv"/>
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106 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="False">
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107 <expand macro="input_centwaveAdvROI" optional="true"/>
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108 </section>
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109 </section>
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110 </when>
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111
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112 <!-- MatchedFilter -->
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113 <when value="MatchedFilter">
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114 <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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115 <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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116 <section name="MatchedFilterAdv" title="Advanced Options" expanded="False">
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117 <conditional name="impute_cond">
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118 <param argument="impute" type="select" label="Method to be used for missing value imputation" help="(previously profmethod)">
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119 <option value="none">none - no linear interpolation</option>
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120 <option value="lin">lin - linear interpolation</option>
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121 <option value="linbase">linbase - linear interpolation within a certain bin-neighborhood</option>
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122 <option value="intlin">intlin - integral of the linearly interpolated data from plus to minus half the step size</option>
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123 </param>
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124 <when value="none" />
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125 <when value="lin" />
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126 <when value="linbase">
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127 <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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128 <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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129 </when>
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130 <when value="intlin" />
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131 </conditional>
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132 <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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133 <param argument="max" type="integer" value="5" label="Maximum number of peaks that are expected/will be identified per slice" />
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134 <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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135 <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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136 <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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137 <!-- index -->
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138 </section>
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139 </when>
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140
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141 <!-- CentWaveWithPredIsoROIs -->
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142 <when value="CentWavePredIso">
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143 <expand macro="input_centwave"/>
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144 <section name="CentWaveAdv" title="Advanced Options" expanded="False">
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145 <expand macro="input_centwaveAdv"/>
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146 </section>
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147 <section name="CentWaveAdvROI" title="List of regions-of-interest (ROI)" expanded="True">
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148 <expand macro="input_centwaveAdvROI" optional="true" />
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149 <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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150 <param argument="maxCharge" type="integer" value="3" label="Maximal isotope charge" help="Isotopes will be defined for charges ‘1:maxCharge’." />
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151 <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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152 <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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153 <param argument="polarity" type="select" label="Polarity of the data">
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154 <option value="unknown">unknown</option>
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155 <option value="positive">positive</option>
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156 <option value="negative">negative</option>
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157 </param>
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158 </section>
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159 </when>
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160
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161 <!-- MSW -->
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162 <when value="MSW">
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163 <!---@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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164 <param argument="snthresh" type="integer" value="3" label="Signal to Noise ratio cutoff" help="" />
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165 <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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166 <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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167 <expand macro="input_validator_list_integer"/>
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168 </param>
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169 <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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170 <!-- peakScaleRange -->
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171 <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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172 <!-- minNoiseLevel -->
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173 <!-- ridgeLength -->
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174 <!-- peakThr -->
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175 <!-- tuneIn -->
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176 <!---@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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177 </when>
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178 </conditional>
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179
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180 <expand macro="input_file_load"/>
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181 </inputs>
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182
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183 <outputs>
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184 <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
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185 <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
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186 </outputs>
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187
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188 <tests>
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189
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190 <!--<test>
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191 <param name="image" value="faahKO.raw.Rdata" ftype="rdata" />
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192 <section name="filterSection">
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193 <param name="filterAcquisitionNum" value="100,5000" />
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194 <param name="filterRt" value="3000,4000" />
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195 <param name="filterMz" value="300,400" />
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196 </section>
32
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197 <conditional name="methods">
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198 <param name="method" value="CentWave" />
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199 <param name="ppm" value="25" />
35
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200 <param name="peakwidth" value="20,50" />-->
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201 <!-- DISABLE: just for testing the arguments
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202 <section name="CentWaveAdv">
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203 <section name="CentWaveAdvROI">
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204 <param name="roiList" value="roiList.txt" ftype="tabular" />
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205 </section>
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206 </section>-->
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207 <!--</conditional>
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208 <expand macro="test_file_load_zip"/>
32
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209 <assert_stdout>
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210 <has_text text="ppm: 25" />
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211 <has_text text="peakwidth: 20, 50" />
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212 <has_text text="object with 4 samples" />
33
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213 <has_text text="Time range: 3006.9-3978.7 seconds (50.1-66.3 minutes)" />
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214 <has_text text="Mass range: 300-400 m/z" />
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215 <has_text text="Peaks: 1311 (about 328 per sample)" />
32
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216 <has_text text="Peak Groups: 0" />
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217 <has_text text="Sample classes: KO, WT" />
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218 </assert_stdout>
35
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219 </test>-->
6
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220 <test>
37
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221 <param name="image" value="ko15-raw.RData" ftype="rdata" />
32
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222 <conditional name="methods">
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223 <param name="method" value="CentWave" />
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224 <param name="ppm" value="25" />
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225 <param name="peakwidth" value="20,50" />
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226 </conditional>
35
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227 <expand macro="test_file_load_single_ko15"/>
32
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228 <assert_stdout>
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229 <has_text text="ppm: 25" />
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230 <has_text text="peakwidth: 20, 50" />
32
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231 <has_text text="object with 1 samples" />
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232 <has_text text="Time range: 2506.1-4471.7 seconds (41.8-74.5 minutes)" />
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233 <has_text text="Mass range: 200.2-600 m/z" />
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234 <has_text text="Peaks: 2262 (about 2262 per sample)" />
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235 <has_text text="Peak Groups: 0" />
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236 <has_text text="Sample classes: ." />
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237 </assert_stdout>
31
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238 </test>
35
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239 <!-- DISABLE FOR TRAVIS
37
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240 Useful to generate test-data for the further steps
31
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241 <test>
37
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242 <param name="image" value="ko16-raw.RData" ftype="rdata" />
32
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243 <conditional name="methods">
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244 <param name="method" value="CentWave" />
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245 <param name="ppm" value="25" />
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246 <param name="peakwidth" value="20,50" />
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247 </conditional>
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248 <assert_stdout>
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249 <has_text text="object with 1 samples" />
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lecorguille
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250 <has_text text="Time range: 2521.7-4477.9 seconds (42-74.6 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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251 <has_text text="Mass range: 200.1-600 m/z" />
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252 <has_text text="Peaks: 2408 (about 2408 per sample)" />
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253 <has_text text="Peak Groups: 0" />
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254 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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255 </assert_stdout>
31
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256 </test>
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257 <test>
37
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258 <param name="image" value="wt15-raw.RData" ftype="rdata" />
32
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259 <conditional name="methods">
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260 <param name="method" value="CentWave" />
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261 <param name="ppm" value="25" />
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262 <param name="peakwidth" value="20,50" />
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263 </conditional>
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264 <assert_stdout>
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265 <has_text text="object with 1 samples" />
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266 <has_text text="Time range: 2517-4473.2 seconds (42-74.6 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
267 <has_text text="Mass range: 200.2-599.8 m/z" />
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lecorguille
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268 <has_text text="Peaks: 2278 (about 2278 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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269 <has_text text="Peak Groups: 0" />
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270 <has_text text="Sample classes: ." />
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271 </assert_stdout>
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272 </test>
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273 <test>
37
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274 <param name="image" value="wt16-raw.RData" ftype="rdata" />
32
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275 <conditional name="methods">
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276 <param name="method" value="CentWave" />
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277 <param name="ppm" value="25" />
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278 <param name="peakwidth" value="20,50" />
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279 </conditional>
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280 <assert_stdout>
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diff changeset
281 <has_text text="object with 1 samples" />
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lecorguille
parents: 31
diff changeset
282 <has_text text="Time range: 2521.7-4468.5 seconds (42-74.5 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
283 <has_text text="Mass range: 200.3-600 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
284 <has_text text="Peaks: 2303 (about 2303 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
285 <has_text text="Peak Groups: 0" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
286 <has_text text="Sample classes: ." />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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287 </assert_stdout>
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288 </test>
37
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diff changeset
289 -->
32
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290 <!-- DISABLE FOR TRAVIS
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291 Test to test the different methods parameters
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292 <test>
37
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293 <param name="image" value="ko15-raw.RData" ftype="rdata" />
32
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294 <conditional name="methods">
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295 <param name="method" value="MatchedFilter" />
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296 <param name="fwhm" value="35" />
37
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297 <section name="MatchedFilterAdv"
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298 <conditional name="impute_cond">
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299 <param name="impute" value="linbase" />
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300 <param name="baseValue" value="0.1" />
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301 <param name="distance" value="1" />
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302 </conditional>
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303 </section>
32
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304 </conditional>
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305 <assert_stdout>
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306 <has_text text="fwhm: 35" />
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307 <has_text text="impute: linbase" />
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308 <has_text text="baseValue: 0.1" />
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309 <has_text text="distance: 1" />
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310 </assert_stdout>
31
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311 </test>
17
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312 <test>
37
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313 <param name="image" value="ko15-raw.RData" ftype="rdata" />
35
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314 <conditional name="methods">
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315 <param name="method" value="CentWavePredIso" />
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316 <param name="ppm" value="56" />
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317 <param name="peakwidth" value="5.275,13.5" />
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318 <section name="CentWaveAdvROI">
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319 <param name="roiList" value="roiList.txt" ftype="tabular" />
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320 </section>
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321 </conditional>
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322 <assert_stdout>
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323 <has_text text=" scmin scmax mzmin mzmax length intensity" />
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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324 <has_text text="1 200 300 300 350 100 5000" />
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325 </assert_stdout>
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326 </test>
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327 <test>
37
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328 <param name="image" value="ko15-raw.RData" ftype="rdata" />
32
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329 <conditional name="methods">
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330 <param name="method" value="MSW" />
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331 <param name="snthresh" value="4" />
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332 <param name="verboseColumns" value="true" />
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333 </conditional>
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334 <assert_stdout>
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335 <has_text text="snthresh: 4" />
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336 <has_text text="verboseColumns: TRUE" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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337 </assert_stdout>
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338 </test>
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339 -->
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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340 <!-- DISABLE FOR TRAVIS
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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341 No more test-data/sacuri_dir_root.zip
17
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342 <test>
35
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343 <param name="image" value="sacuri_dir_root.zip" ftype="zip" />
32
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344 <conditional name="methods">
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345 <param name="method" value="MatchedFilter" />
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346 <param name="step" value="0.01" />
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347 <param name="fwhm" value="4" />
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348 <conditional name="options_m">
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349 <param name="option" value="show" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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350 <param name="max" value="50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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351 <param name="snthresh" value="1" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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352 <param name="steps" value="2" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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353 </conditional>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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354 </conditional>
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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355 <assert_stdout>
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356 <has_text text="object with 4 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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357 <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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358 <has_text text="Mass range: 50.0021-999.9863 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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359 <has_text text="Peaks: 59359 (about 14840 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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360 <has_text text="Peak Groups: 0" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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361 <has_text text="Sample classes: bio, blank" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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362 </assert_stdout>
17
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363 </test>
32
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364 -->
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
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365 <!-- DISABLE FOR TRAVIS
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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366 No more test-data/sacuri_current_root.zip
17
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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367 <test>
35
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368 <param name="image" value="sacuri_current_root.zip" ftype="zip" />
32
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369 <conditional name="methods">
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370 <param name="method" value="CentWave" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
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diff changeset
371 <param name="ppm" value="25" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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372 <param name="peakwidth" value="20,50" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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373 </conditional>
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374 <assert_stdout>
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lecorguille
parents: 31
diff changeset
375 <has_text text="object with 4 samples" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
376 <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
377 <has_text text="Mass range: 57.9756-593.4086 m/z" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
378 <has_text text="Peaks: 1535 (about 384 per sample)" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
379 <has_text text="Peak Groups: 0" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
380 <has_text text="Sample classes: bio, blank" />
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
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diff changeset
381 </assert_stdout>
17
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diff changeset
382 </test>
32
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diff changeset
383 -->
0
1bad16e5e4ae planemo upload
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diff changeset
384 </tests>
15
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lecorguille
parents: 13
diff changeset
385
1
2f5b78be1dd6 Uploaded
lecorguille
parents: 0
diff changeset
386 <help><![CDATA[
0
1bad16e5e4ae planemo upload
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387
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388 @HELP_AUTHORS@
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389
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390 ===================
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391 xcms findChromPeaks
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392 ===================
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393
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394 -----------
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395 Description
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396 -----------
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397
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398 This tool is used for preprocessing data from multiple LC/MS files (NetCDF, mzXML and mzData formats) using the xcms_ R package. It extracts ions from each sample independently, and using a statistical model, peaks are filtered and integrated.
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399 A tutorial on how to perform xcms preprocessing is available here_.
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400
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401 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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402 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
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403
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404
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405 -----------------
0
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406 Workflow position
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407 -----------------
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408
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409 **Upstream tools**
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410
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411 ========================= ================= ==============================
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412 Name Output file Format
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413 ========================= ================= ==============================
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414 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
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415 ========================= ================= ==============================
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416
0
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417
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418 **Downstream tools**
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419
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420 ==================================== ======================== =========================
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421 Name Output file Format
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422 ==================================== ======================== =========================
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423 xcms.findChromPeaks Merger (single) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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424 ------------------------------------ ------------------------ -------------------------
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425 xcms.groupChromPeaks (zip) ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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426 ==================================== ======================== =========================
0
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427
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428
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429 **Example of a metabolomic workflow**
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430
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431 .. image:: xcms_xcmsset_workflow.png
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432
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433 ---------------------------------------------------
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434
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435 ----------
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436 Parameters
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437 ----------
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438
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439 Extraction method for peaks detection
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440 -------------------------------------
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441
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442 **MatchedFilter**
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443
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444 | 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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445 | See the MatchedFilter_manual_
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446
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447 **CentWave**
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448
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449 | 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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450 | Due to the fact that peak centroids are used, a binning step is not necessary.
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451 | 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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452 | See the CentWave_manual_
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453
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454 **CentWaveWithPredIsoROIs**
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455
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456 | 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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457 | See the CentWaveWithPredIsoROIs_manual_
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458
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459 **MSW**
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460
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461 | 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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462 | See the MSW_manual_
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463
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464 .. _MatchedFilter_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-matchedFilter.html#heading-2
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465 .. _CentWave_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWave.html#heading-2
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466 .. _CentWaveWithPredIsoROIs_manual: https://rdrr.io/bioc/xcms/man/findChromPeaks-centWaveWithPredIsoROIs.html#heading-2
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467 .. _MSW_manual: https://rdrr.io/bioc/xcms/man/findPeaks-MSW.html#heading-2
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468
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469 @HELP_XCMS_MANUAL@
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470
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471 ------------
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472 Output files
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473 ------------
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474
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475 xset.RData: rdata.xcms.findchrompeaks format
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476
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477 | (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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478 | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".
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479
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480 ---------------------------------------------------
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481
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482 Changelog/News
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483 --------------
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484
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485 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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486
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487 **Version 3.4.4.1 - 30/04/2019**
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488
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489 - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms.
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490
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491 **Version 3.4.4.0 - 08/02/2019**
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492
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493 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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494
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495
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496 **Version 3.0.0.0 - 08/03/2018**
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497
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498 - 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.
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499
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500 - CHANGE: xcms.findChromPeaks no longer read the raw data. You have to run MSnbase readMSData first.
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501
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502 - NEW: a bunch of new options: Spectra Filters (previously scanrange), CentWave.(mzCenterFun, fitgauss, verboseColumns), MatchedFilter.(sigma, impute, baseValue, max), MSW.(verboseColumns), ...
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503
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504 - NEW: new Filters for Spectra
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505
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506 - NEW: new methods: CentWaveWithPredIsoROIs
7f636ad1162b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
parents: 34
diff changeset
507
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
508 - 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
509
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
510 - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values.
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2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
511
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efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
512 - 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
513
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
514 - 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
515
32
2bf1cb023c94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
lecorguille
parents: 31
diff changeset
516
31
e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 30
diff changeset
517 **Version 2.1.1 - 29/11/2017**
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5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 28
diff changeset
518
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e93153c07be0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
lecorguille
parents: 30
diff changeset
519 - 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
520
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efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
521
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626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
lecorguille
parents: 25
diff changeset
522 **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
523
602acc32b549 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 16
diff changeset
524 - 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
525
26
626d3db664ef planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
lecorguille
parents: 25
diff changeset
526 - 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
527
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
528
16
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
529 **Version 2.0.11 - 22/12/2016**
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
530
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
531 - BUGFIX: propose scanrange for all methods
f28041d2180a planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 15
diff changeset
532
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efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
533
15
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
534 **Version 2.0.10 - 22/12/2016**
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
535
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
536 - 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
537
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
538
13
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
539 **Version 2.0.9 - 06/07/2016**
68547432079b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
540
15
1a9bbd4670e8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 13
diff changeset
541 - 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
542
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efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
543
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
544 **Version 2.0.8 - 06/04/2016**
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
545
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
546 - TEST: refactoring to pass planemo test using conda dependencies
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
547
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
548
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
549 **Version 2.0.7 - 10/02/2016**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
550
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
551 - BUGFIX: better management of errors. Datasets remained green although the process failed
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
552
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
553 - 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
554
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
555 - 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
556
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
557 - UPDATE: refactoring of internal management of inputs/outputs
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
558
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
559 - TEST: refactoring to feed the new report tool
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
560
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
561
29
5dba1c94fb94 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
lecorguille
parents: 28
diff changeset
562 **Version 2.0.2 - 18/01/2016**
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
563
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
564 - 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
565
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
566
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
567 **Version 2.0.2 - 09/10/2015**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
568
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
569 - 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
570
34
efd23113d5f4 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309
lecorguille
parents: 33
diff changeset
571
4
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
572 **Version 2.0.2 - 02/06/2015**
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
573
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
574 - 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
575
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
576 - 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
577
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
578 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4509e9dd03e4 planemo upload
lecorguille
parents: 3
diff changeset
579
1
2f5b78be1dd6 Uploaded
lecorguille
parents: 0
diff changeset
580 ]]></help>
0
1bad16e5e4ae planemo upload
lecorguille
parents:
diff changeset
581
6
60f6c208ca16 planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
582 <expand macro="citation" />
0
1bad16e5e4ae planemo upload
lecorguille
parents:
diff changeset
583 </tool>