Mercurial > repos > lecorguille > xcms_retcor

annotate abims_xcms_retcor.xml @ 34:9714270678a7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:39:48 -0400
parents 69b5a006fca1
children 35a20d7c9f33
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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 <import>macros_xcms.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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13 <command><![CDATA[
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14 @COMMAND_RSCRIPT@/xcms_retcor.r
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15 image '$image'
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17 method $methods.method
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18 #if $methods.method == "PeakGroups":
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19 minFraction $methods.minFraction
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20 extraPeaks $methods.extraPeaks
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21 smooth $methods.smooth_cond.smooth
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22 ## PeakGroupsSmoothLoess Advanced
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23 span $methods.smooth_cond.PeakGroupsSmoothLoessAdv.span
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24 family $methods.smooth_cond.PeakGroupsSmoothLoessAdv.family
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25 #else
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26 binSize $methods.binSize
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27 ## Advanced
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28 #if $methods.ObiwarpAdv.centerSample != "":
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29 centerSample $methods.ObiwarpAdv.centerSample
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30 #end if
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31 response $methods.ObiwarpAdv.response
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32 distFun $methods.ObiwarpAdv.distFunCond.distFun
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33 gapInit $methods.ObiwarpAdv.distFunCond.gapInit
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34 gapExtend $methods.ObiwarpAdv.distFunCond.gapExtend
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35 factorDiag $methods.ObiwarpAdv.factorDiag
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36 factorGap $methods.ObiwarpAdv.factorGap
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37 localAlignment $methods.ObiwarpAdv.localAlignmentCond.localAlignment
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38 initPenalty $methods.ObiwarpAdv.localAlignmentCond.initPenalty
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39 #end if
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41 @COMMAND_FILE_LOAD@
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43 @COMMAND_LOG_EXIT@
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44 ]]></command>
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46 <inputs>
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47 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
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48 <conditional name="methods">
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49 <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
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50 <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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51 <option value="Obiwarp">Obiwarp - alignment based on the complete mz-rt data.</option>
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52 </param>
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53 <when value="PeakGroups">
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54 <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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55 <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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56 <conditional name="smooth_cond">
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57 <param argument="smooth" type="select" label="Smooth method" >
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58 <option value="loess" selected="true">loess - non-linear alignment</option>
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59 <option value="linear">linear - linear alignment</option>
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60 </param>
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61 <when value="loess">
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62 <section name="PeakGroupsSmoothLoessAdv" title="Advanced Options" expanded="False">
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63 <param argument="span" type="float" value="0.2" label="Degree of smoothing for the loess fitting" />
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64 <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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65 <option value="gaussian" selected="true">gaussian</option>
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66 <option value="symmetric">symmetric</option>
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67 </param>
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68 </section>
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69 </when>
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70 <when value="linear" />
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71 </conditional>
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72 </when>
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73 <when value="Obiwarp">
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74 <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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75 <section name="ObiwarpAdv" title="Advanced Options" expanded="False">
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76 <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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77 <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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78 <conditional name="distFunCond">
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79 <param argument="distFun" type="select" label="Distance function to be used">
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80 <option value="cor_opt" selected="true">cor_opt - calculate only 10% diagonal band of distance matrix; better runtime</option>
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81 <option value="cor">cor - Pearson's correlation</option>
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82 <option value="cov">cov - covariance</option>
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83 <option value="prd">prd - product</option>
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84 <option value="euc">euc - Euclidian distance</option>
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85 </param>
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86 <when value="cor_opt">
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87 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
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88 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
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89 </when>
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90 <when value="cor">
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91 <param argument="gapInit" type="float" value="0.3" label="Penalty for gap opening" />
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92 <param argument="gapExtend" type="float" value="2.4" label="Penalty for gap enlargement" />
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93 </when>
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94 <when value="cov">
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95 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
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96 <param argument="gapExtend" type="float" value="11.7" label="Penalty for gap enlargement" />
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97 </when>
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98 <when value="prd">
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99 <param argument="gapInit" type="float" value="0.0" label="Penalty for gap opening" />
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100 <param argument="gapExtend" type="float" value="7.8" label="Penalty for gap enlargement" />
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101 </when>
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102 <when value="euc">
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103 <param argument="gapInit" type="float" value="0.9" label="Penalty for gap opening" />
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104 <param argument="gapExtend" type="float" value="1.8" label="Penalty for gap enlargement" />
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105 </when>
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106 </conditional>
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107 <param argument="factorDiag" type="float" value="2" label="Local weight applied to diagonal moves in the alignment" />
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108 <param argument="factorGap" type="float" value="1" label="local weight for gap moves in the alignment" />
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109 <conditional name="localAlignmentCond">
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110 <param argument="localAlignment" type="select" label="Whether a local alignment should be performed instead of the default global alignment">
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111 <option value="FALSE" selected="true">FALSE</option>
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112 <option value="TRUE">TRUE</option>
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113 </param>
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114 <when value="FALSE">
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115 <param argument="initPenalty" type="hidden" value="0" label="Penalty for initiating an alignment" />
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116 </when>
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117 <when value="TRUE">
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118 <param argument="initPenalty" type="float" value="0" label="Penalty for initiating an alignment" />
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119 </when>
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120 </conditional>
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121 </section>
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122 </when>
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123 </conditional>
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124
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125 <expand macro="input_file_load"/>
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126
0
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127 </inputs>
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128
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129 <outputs>
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130 <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" from_work_dir="retcor.RData" />
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131 <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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132 </outputs>
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133
0
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134 <tests>
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135 <test>
34
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136 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
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137 <conditional name="methods">
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138 <param name="method" value="PeakGroups"/>
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139 <param name="extraPeaks" value="1"/>
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140 <param name="minFraction" value="1"/>
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141 <conditional name="smooth_cond">
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142 <param name="smooth" value="loess"/>
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143 <section name="PeakGroupsSmoothLoessAdv">
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144 <param name="span" value="0.2"/>
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145 <param name="family" value="gaussian"/>
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146 </section>
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147 </conditional>
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148 </conditional>
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149 <expand macro="test_file_load_single"/>
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150 <assert_stdout>
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151 <has_text text="extraPeaks: 1" />
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152 <has_text text="minFraction: 1" />
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153 <has_text text="span: 0.2" />
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154 <has_text text="object with 4 samples" />
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155 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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156 <has_text text="Mass range: 200.1-600 m/z" />
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157 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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158 <has_text text="Peak Groups: 0" />
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159 <has_text text="Sample classes: KO, WT" />
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160 </assert_stdout>
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161 </test>
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162 <!-- DISABLE FOR TRAVIS : Zip
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163 <test>
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164 <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/>
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165 <conditional name="methods">
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166 <param name="method" value="PeakGroups"/>
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167 <param name="extraPeaks" value="1"/>
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168 <param name="minFraction" value="1"/>
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169 <conditional name="smooth_cond">
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170 <param name="smooth" value="loess"/>
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171 <section name="PeakGroupsSmoothLoessAdv">
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172 <param name="span" value="0.2"/>
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173 <param name="family" value="gaussian"/>
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174 </section>
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175 </conditional>
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176 </conditional>
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177 <expand macro="test_file_load_zip"/>
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178 <assert_stdout>
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179 <has_text text="object with 4 samples" />
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180 <has_text text="Time range: 2509.2-4480.3 seconds (41.8-74.7 minutes)" />
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181 <has_text text="Mass range: 200.1-600 m/z" />
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182 <has_text text="Peaks: 9251 (about 2313 per sample)" />
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183 <has_text text="Peak Groups: 0" />
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184 <has_text text="Sample classes: KO, WT" />
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185 </assert_stdout>
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186 </test>
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187 -->
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188 <!-- DISABLE FOR TRAVIS
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189 Test to test the different methods parameters
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190 <test>
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191 <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
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192 <conditional name="methods">
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193 <param name="method" value="Obiwarp"/>
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194 <section name="ObiwarpAdv">
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195 <param name="centerSample" value="1"/>
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196 <param name="response" value="0"/>
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197 <conditional name="distFunCond">
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198 <param name="distFun" value="cov"/>
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199 <param name="gapInit" value="0.1" />
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200 </conditional>
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201 </section>
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202 </conditional>
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203 <expand macro="test_file_load_single"/>
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204 <assert_stdout>
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205 <has_text text="centerSample: 1" />
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206 <has_text text="response: 0" />
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207 <has_text text="distFun: cov" />
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208 <has_text text="gapInit: 0.1" />
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209 <has_text text="gapExtend: 11.7" />
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210 </assert_stdout>
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211 </test>
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212 -->
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213 </tests>
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214
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f42bd3de6aad Uploaded
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215 <help><![CDATA[
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216
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217 @HELP_AUTHORS@
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218
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219 ================
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220 xcms adjustRtime
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221 ================
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222
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223 -----------
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224 Description
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225 -----------
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226
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227 After matching peaks into groups, xcms can use those groups to identify and correct
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228 correlated drifts in retention time from run to run. The aligned peaks can then be
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229 used for a second pass of peak grouping which will be more accurate than the first.
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230 The whole process can be repeated in an iterative fashion. Not all peak groups will be helpful
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231 for identifying retention time drifts. Some groups may be missing peaks from a large
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232 fraction of samples and thus provide an incomplete picture of the drift at that time point.
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233 Still others may contain multiple peaks from the same sample, which is a sign of impropper grouping.
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234
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235 .. class:: warningmark
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236
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237 **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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238 discarded)**
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239
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240
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241
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242 -----------------
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243 Workflow position
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244 -----------------
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245
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246
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247 **Upstream tools**
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248
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249 ========================= ================= ============================== ==========
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250 Name output file format parameter
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251 ========================= ================= ============================== ==========
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252 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
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253 ------------------------- ----------------- ------------------------------ ----------
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254 xcms.group xset.group.RData RData RData file
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255 ========================= ================= ============================== ==========
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256
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257
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258 **Downstream tools**
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259
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260 =========================== ================== ========
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261 Name Output file Format
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262 =========================== ================== ========
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263 xcms.group xset.retcor.RData RData
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264 =========================== ================== ========
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265
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266
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267 **General schema of the metabolomic workflow**
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268
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269 .. image:: xcms_retcor_workflow.png
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270
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271 ---------------------------------------------------
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272
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273 ----------
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274 Parameters
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275 ----------
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276
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277 Method
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278 ------
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279
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280 **PeakGroups**
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281
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282 | 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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283 | See the PeakGroups_manual_
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284
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285 **Obiwarp**
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286
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287 | 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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288 | See the Obiwarp_manual_
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289
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290 .. _PeakGroups_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-peakGroups.html#heading-2
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291 .. _Obiwarp_manual: https://rdrr.io/bioc/xcms/man/adjustRtime-obiwarp.html
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292
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293 @HELP_XCMS_MANUAL@
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294
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295 ------------
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296 Output files
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297 ------------
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298
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299 xset.group.retcor.RData: rdata.xcms.retcor format
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300
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301 | Rdata file that will be necessary in the **xcms.group** step of the workflow.
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302
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303
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304 ---------------------------------------------------
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305
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306 Changelog/News
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307 --------------
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308
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309 **Version 3.0.0.0 - 08/03/2018**
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310
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311 - 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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312
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313 - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty)
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314
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315 - 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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316
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317 - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram"
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318
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319
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c013ed353a2f planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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320 **Version 2.1.1 - 29/11/2017**
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30410a052ab3 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9
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321
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322 - 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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323
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324
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325 **Version 2.1.0 - 03/02/2017**
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326
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327 - IMPROVEMENT: xcms.retcor can deal with merged individual data
20a75ba4345b planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
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328
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329
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330 **Version 2.0.8 - 22/12/2016**
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331
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332 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
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333
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334
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aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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335 **Version 2.0.7 - 06/07/2016**
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336
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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337 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
aee5648dc924 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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338
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339
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340 **Version 2.0.6 - 04/04/2016**
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341
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342 - TEST: refactoring to pass planemo test using conda dependencies
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343
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344
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345 **Version 2.0.5 - 10/02/2016**
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346
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347 - BUGFIX: better management of errors. Datasets remained green although the process failed
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348
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349 - BUGFIX: some pdf remained empty even when the process succeed
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350
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351 - UPDATE: refactoring of internal management of inputs/outputs
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352
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353 - UPDATE: refactoring to feed the new report tool
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354
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355
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356 **Version 2.0.2 - 02/06/2015**
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357
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358 - 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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359
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360 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
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361
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362
1
f42bd3de6aad Uploaded
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363 ]]></help>
0
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364
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fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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365
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366 <expand macro="citation" />
0
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367
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368 </tool>