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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e
author lecorguille
date Thu, 01 Mar 2018 04:16:45 -0500
parents c013ed353a2f
children 281786a7b9a2
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1 <tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@WRAPPER_VERSION@.0">
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3 <description>Retention Time Correction</description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 @COMMAND_XCMS_SCRIPT@/xcms_retcor.r
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14 image '$image'
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16 method $methods.method
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17 #if $methods.method == "PeakGroups":
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18 minFraction $methods.minFraction
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19 extraPeaks $methods.extraPeaks
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20 smooth $methods.smooth_cond.smooth
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21 ## PeakGroupsSmoothLoess Advanced
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22 span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span
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23 family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family
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24 #else
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25 binSize $methods.binSize
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26 ## Advanced
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27 #if $methods.ObiwarpAdv.centerSample != "":
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28 centerSample $methods.ObiwarpAdv.centerSample
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29 #end if
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30 response $methods.ObiwarpAdv.response
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31 distFun $methods.ObiwarpAdv.distFunCond.distFun
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32 gapInit $methods.ObiwarpAdv.distFunCond.gapInit
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33 gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend
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34 factorDiag $methods.ObiwarpAdv.factorDiag
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35 factorGap $methods.ObiwarpAdv.factorGap
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36 localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment
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37 initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty
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38 #end if
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40 @COMMAND_FILE_LOAD@
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42 @COMMAND_LOG_EXIT@
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43 ]]></command>
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44
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45 <inputs>
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46 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
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47 <conditional name="methods">
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48 <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
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49 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
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50 <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>
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51 </param>
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52 <when value="PeakGroups">
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53 <param argument="minFraction" type="float" value="0.9" min="0" max="1" label="Minimum required fraction of samples in which peaks for the peak group were identified" help="(previously missing)"/>
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54 <param argument="extraPeaks" type="integer" value="1" label="Maximal number of additional peaks for all samples to be assigned to a peak group for retention time correction" help="For a data set with 6 samples, ‘extraPeaks = 1’ uses all peak groups with a total peak count lower or equal to ‘6 + 1’. The total peak count is the total number of peaks being assigned to a peak group and considers also multiple peaks within a sample being assigned to the group. (previously extra)" />
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55 <conditional name="smooth_cond">
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56 <param argument="smooth" type="select" label="Smooth method" >
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57 <option value="loess" selected="true">loess - non-linear alignment</option>
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58 <option value="linear">linear - linear alignment</option>
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59 </param>
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60 <when value="loess">
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61 <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">
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62 <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />
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63 <param argument="family" type="select" label="Family" help="if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
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64 <option value="gaussian" selected="true">gaussian</option>
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65 <option value="symmetric">symmetric</option>
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66 </param>
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67 </section>
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68 </when>
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69 <when value="linear" />
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70 </conditional>
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71 </when>
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72 <when value="Obiwarp">
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73 <param argument="binSize" type="float" value="1" label="Bin size (in mz dimension) to be used for the profile matrix generation" help="See ‘step’ parameter in ‘profile-matrix’ documentation for more details. (previously profStep)" />
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74 <section name="ObiwarpAdv" title="Advanced Options" expanded="False">
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75 <param argument="centerSample" type="integer" value="" optional="true" label="Index of the center sample in the experiment" help="It defaults to ‘floor(median(1:length(fileNames(object))))’" />
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76 <param argument="response" type="integer" value="1" label="Defining the responsiveness of warping" help="with ‘response = 0’ giving linear warping on start and end points and ‘response = 100’ warping using all bijective anchors." />
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77 <conditional name="distFunCond">
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78 <param argument="distFun" type="select" label="Distance function to be used">
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79 <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option>
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80 <option value="cor">cor - Pearson's correlation</option>
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81 <option value="cov">cov - covariance</option>
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82 <option value="prd">prd - product</option>
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83 <option value="euc">euc - Euclidian distance</option>
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84 </param>
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85 <when value="cor_opt">
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86 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
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87 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
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88 </when>
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89 <when value="cor">
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90 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
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91 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
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92 </when>
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93 <when value="cov">
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94 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
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95 <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" />
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96 </when>
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97 <when value="prd">
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98 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
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99 <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" />
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100 </when>
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101 <when value="euc">
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102 <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" />
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103 <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" />
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104 </when>
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105 </conditional>
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106 <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" />
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107 <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" />
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108 <conditional name="localAlignmentCond">
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109 <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment">
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110 <option value="FALSE" selected="true">FALSE</option>
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111 <option value="TRUE">TRUE</option>
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112 </param>
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113 <when value="FALSE">
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114 <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" />
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115 </when>
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116 <when value="TRUE">
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117 <param argument="initPenalty" type="float" value="0" label="Penalty for initiating an alignment" />
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118 </when>
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119 </conditional>
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120 </section>
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121 </when>
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122 </conditional>
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123
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124 <expand macro="input_file_load"/>
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125
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126 </inputs>
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127
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128 <outputs>
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129 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" from_work_dir="retcor.RData" />
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130 <data name="rawVSadjustedPdf" format="pdf" label="${image.name[:-6]}_rawVSadjusted.retcor.Rplots.pdf" from_work_dir="raw_vs_adjusted_rt.pdf" />
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131 <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" from_work_dir="TICs.pdf"/>
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132 <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" from_work_dir="BICs.pdf" />
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133 </outputs>
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134
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135 <tests>
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136 <test>
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137 <param name="image" value="faahKO-single-class.xset.group.RData"/>
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138 <conditional name="methods">
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139 <param name="method" value="PeakGroups"/>
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140 <param name="extraPeaks" value="1"/>
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141 <param name="minFraction" value="1"/>
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142 <conditional name="smooth_cond">
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143 <param name="smooth" value="loess"/>
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144 <section name="PeakGroupsSmoothLoessAdv">
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145 <param name="span" value="0.2"/>
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146 <param name="family" value="gaussian"/>
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147 </section>
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148 </conditional>
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149 </conditional>
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150 <expand macro="test_file_load_single"/>
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151 <assert_stdout>
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152 <has_text text="extraPeaks: 1" />
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153 <has_text text="minFraction: 1" />
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154 <has_text text="span: 0.2" />
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155 <has_text text="object with 4 samples" />
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156 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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157 <has_text text="Mass range: 200.1-600 m/z" />
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158 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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159 <has_text text="Peak Groups: 0" />
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160 <has_text text="Sample classes: KO, WT" />
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161 </assert_stdout>
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162 </test>
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163 <!-- DISABLE FOR TRAVIS : Zip
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164 <test>
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165 <param name="image" value="faahKO.xset.group.RData"/>
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166 <conditional name="methods">
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167 <param name="method" value="PeakGroups"/>
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168 <param name="extraPeaks" value="1"/>
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169 <param name="minFraction" value="1"/>
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170 <conditional name="smooth_cond">
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171 <param name="smooth" value="loess"/>
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172 <section name="PeakGroupsSmoothLoessAdv">
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173 <param name="span" value="0.2"/>
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174 <param name="family" value="gaussian"/>
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175 </section>
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176 </conditional>
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177 </conditional>
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178 <expand macro="test_file_load_zip"/>
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179 <assert_stdout>
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180 <has_text text="object with 4 samples" />
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181 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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182 <has_text text="Mass range: 200.1-600 m/z" />
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183 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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184 <has_text text="Peak Groups: 0" />
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185 <has_text text="Sample classes: KO, WT" />
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186 </assert_stdout>
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187 </test>
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188 -->
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189 <!-- DISABLE FOR TRAVIS
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190 Test to test the different methods parameters
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191 <test>
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192 <param name="image" value="faahKO-single-class.xset.group.RData"/>
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193 <conditional name="methods">
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194 <param name="method" value="Obiwarp"/>
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195 <section name="ObiwarpAdv">
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196 <param name="centerSample" value="1"/>
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197 <param name="response" value="0"/>
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198 <conditional name="distFunCond">
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199 <param name="distFun" value="cov"/>
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200 <param name="gapInit" value="0.1" />
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201 </conditional>
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202 </section>
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203 </conditional>
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204 <expand macro="test_file_load_single"/>
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205 <assert_stdout>
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206 <has_text text="centerSample: 1" />
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207 <has_text text="response: 0" />
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208 <has_text text="distFun: cov" />
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209 <has_text text="gapInit: 0.1" />
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210 <has_text text="gapExtend: 11.7" />
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211 </assert_stdout>
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212 </test>
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213 -->
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214 </tests>
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215
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216 <help><![CDATA[
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217
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218 @HELP_AUTHORS@
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219
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220 ================
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221 xcms adjustRtime
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222 ================
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223
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224 -----------
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225 Description
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226 -----------
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227
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228 After matching peaks into groups, xcms can use those groups to identify and correct
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229 correlated drifts in retention time from run to run. The aligned peaks can then be
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230 used for a second pass of peak grouping which will be more accurate than the first.
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231 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
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232 for identifying retention time drifts. Some groups may be missing peaks from a large
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233 fraction of samples and thus provide an incomplete picture of the drift at that time point.
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234 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
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235
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236 .. class:: warningmark
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237
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238 **After an adjustRtime step, it is mandatory to do a groupChromPeaks step, otherwise the rest of the workflow will not work with the RData file. (the initial peak grouping becomes invalid and is
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239 discarded)**
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240
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241
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242
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243 -----------------
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244 Workflow position
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245 -----------------
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246
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247
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248 **Upstream tools**
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249
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250 ========================= ================= ======= ==========
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251 Name output file format parameter
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252 ========================= ================= ======= ==========
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253 xcms.group xset.group.RData RData RData file
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254 ========================= ================= ======= ==========
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255
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256
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257 **Downstream tools**
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258
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259 +---------------------------+------------------+--------+
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260 | Name | Output file | Format |
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261 +===========================+==================+========+
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262 |xcms.group | xset.retcor.RData| RData |
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263 +---------------------------+------------------+--------+
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264
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265 The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
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266
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267
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268 **General schema of the metabolomic workflow**
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269
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270 .. image:: xcms_retcor_workflow.png
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271
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272
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273 -----------
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274 Input files
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275 -----------
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276
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277 +---------------------------+----------------------+
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278 | Parameter : num + label | Format |
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279 +===========================+======================+
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280 | 1 : RData file | rdata.xcms.group |
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281 +---------------------------+----------------------+
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282
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283
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284 ----------
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285 Parameters
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286 ----------
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287
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288 Method
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289 ------
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290
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291 **PeakGroups**
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292
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293 | This method performs retention time adjustment based on the alignment of chromatographic peak groups present in all/most samples (hence corresponding to house keeping compounds). First the retention time deviation of these peak groups is described by fitting either a polynomial (‘smooth = "loess"’) or a linear ( ‘smooth = "linear"’) model to the data points. These models are subsequently used to adjust the retention time of each spectrum in each sample.
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294 | See the PeakGroups_manual_
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295
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296 **Obiwarp**
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297
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298 | This method performs retention time adjustment using the Obiwarp method [Prince 2006]. It is based on the code at http://obi-warp.sourceforge.net but supports alignment of multiple samples by aligning each against a _center_ sample. The alignment is performed directly on the ‘profile-matrix’ and can hence be performed independently of the peak detection or peak grouping.
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299 | See the Obiwarp_manual_
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300
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301 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
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302 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
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303
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304 @HELP_XCMS_MANUAL@
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305
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306 ------------
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307 Output files
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308 ------------
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309
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310 xset.group.retcor.TICs_corrected.pdf
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312 | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
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314 xset.group.retcor.BPCs_corrected.pdf
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316 | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
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317
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318 xset.group.retcor.RData: rdata.xcms.retcor format
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319
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320 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
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321
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323 ------
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325 .. class:: infomark
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327 The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
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328
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329
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330 ---------------------------------------------------
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331
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332 ---------------
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333 Working example
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334 ---------------
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335
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336 Input files
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337 -----------
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338
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339 | RData file -> **xset.group.RData**
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340
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341 Parameters
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342 ----------
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343
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344 | Method: -> **PeakGroups**
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345 | smooth: -> **loess**
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346 | extraPeaks: -> **1**
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347 | minFraction -> **1**
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348 | Advanced options: -> **show**
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349 | span -> **0.2**
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350 | family -> **gaussian**
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351 | plottype -> **deviation**
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354 Output files
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355 ------------
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357 | **1) xset.group.retcor.RData: RData file**
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358
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359 | **2) Example of an xset.group.retcor.TICs_corrected pdf file**
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360
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361 .. image:: xcms_retcor.png
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362
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363
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364 ---------------------------------------------------
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365
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366 Changelog/News
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367 --------------
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368
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369 **Version 3.0.0.0 - 14/02/2018**
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370
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371 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods
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372
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373 **Version 2.1.1 - 29/11/2017**
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374
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375 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
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376
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377 **Version 2.1.0 - 03/02/2017**
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378
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379 - IMPROVEMENT: xcms.retcor can deal with merged individual data
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380
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381 **Version 2.0.8 - 22/12/2016**
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382
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383 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
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384
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385 **Version 2.0.7 - 06/07/2016**
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387 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
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388
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389 **Version 2.0.6 - 04/04/2016**
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391 - TEST: refactoring to pass planemo test using conda dependencies
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393
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394 **Version 2.0.5 - 10/02/2016**
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395
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396 - BUGFIX: better management of errors. Datasets remained green although the process failed
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397
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398 - BUGFIX: some pdf remained empty even when the process succeed
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399
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400 - UPDATE: refactoring of internal management of inputs/outputs
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401
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402 - UPDATE: refactoring to feed the new report tool
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403
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404
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405 **Version 2.0.2 - 02/06/2015**
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406
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407 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
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408
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409 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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410
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411
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f42bd3de6aad Uploaded
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412 ]]></help>
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413
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414
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415 <expand macro="citation" />
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416
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417 </tool>