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annotate qualitymetrics_config.xml @ 2:596320b84315 draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
author ethevenot
date Thu, 11 Jan 2018 12:52:08 -0500
parents 6d3b7b6573d8
children acdf51018708
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596320b84315 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 95d4658e5d9dd0421c9336b2232cc81f32879621
ethevenot
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1 <tool id="quality_metrics" name="Quality Metrics" version="2.2.8">
0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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2 <description>Metrics and graphics to check the quality of the data</description>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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4 <requirements>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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5 <requirement type="package">r-batch</requirement>
1
6d3b7b6573d8 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
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6 <requirement type="package">bioconductor-ropls</requirement>
0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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7 </requirements>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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9 <stdio>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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10 <exit_code range="1:" level="fatal" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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11 </stdio>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13 <command><![CDATA[
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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14 Rscript $__tool_directory__/qualitymetrics_wrapper.R
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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15 dataMatrix_in "$dataMatrix_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 sampleMetadata_in "$sampleMetadata_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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17 variableMetadata_in "$variableMetadata_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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18
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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19 CV "${CV_condition.CV}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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20 #if str($CV_condition.CV ) == 'TRUE':
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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21 Compa "${CV_condition.Compa}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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22 seuil "${CV_condition.seuil}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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23 #else:
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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24 Compa "TRUE"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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25 seuil "1"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 #end if
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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27
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28 #if $advPar.optC == "full"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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29 poolAsPool1L "$advPar.poolAsPool1L"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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30 #else:
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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31 poolAsPool1L "TRUE"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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32 #end if
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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33
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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34 sampleMetadata_out "$sampleMetadata_out"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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35 variableMetadata_out "$variableMetadata_out"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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36 figure "$figure"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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37 information "$information"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 ]]></command>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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39
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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40 <inputs>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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41 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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42 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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43 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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44
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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45 <conditional name="CV_condition">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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46 <param name="CV" type="select" label="Coefficient of Variation" help="">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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47 <option value="FALSE">no</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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48 <option value="TRUE">yes</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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49 </param>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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50 <when value="TRUE">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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51 <param name="Compa" label="Which type of CV calculation should be done" type="select" display="radio" help="">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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52 <option value="TRUE">ratio between pool and sample CVs</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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53 <option value="FALSE">only pool CV</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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54 </param>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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55 <param name="seuil" type="float" label="Threshold" value="1.25" min="0.0000000000000001" help="if comparing pool and sample CVs, corresponds to the max ratio tolerated (basically between 1.0 and 1.25) ; else corresponds to the max pool CV tolerated (basically 0.3)"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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56 </when>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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57 <when value="FALSE">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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58 <param name="Compa" type="hidden" value="TRUE"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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59 <param name="seuil" type="hidden" value="1"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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60 </when>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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61 </conditional>
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62
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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63 <conditional name="advPar">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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64 <param name="optC" type="select" label="Advanced parameters" >
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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65 <option value="default" selected="true">Use default</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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66 <option value="full">Full parameter list</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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67 </param>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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68 <when value="full">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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69 <param name="poolAsPool1L" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use 'pool' samples as 'pool1' when computing the correlation with dilution?"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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70 </when>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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71 <when value="default">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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72 <param name="poolAsPool1L" type="hidden" value="TRUE"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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73 </when>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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74 </conditional>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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75
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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76 </inputs>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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77
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78 <outputs>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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79 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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80 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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81 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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82 <data name="information" label="${tool.name}_information.txt" format="txt"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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83 </outputs>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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84
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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85 <tests>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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86 <test>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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87 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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88 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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89 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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90 <param name="CV" value="FALSE"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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91 <param name="optC" value="default"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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92 <output name="sampleMetadata_out" file="output-sampleMetadata.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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93 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
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94 </test>
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95 </tests>
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96
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97 <help>
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98
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99 .. class:: infomark
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100
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101 **Authors** Marion Landi, Melanie Petera and Etienne Thevenot (W4M Core Development Team)
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102
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103 ---------------------------------------------------
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104
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105 .. class:: infomark
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106
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107 **Tool updates**
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108
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109 See the **NEWS** section at the bottom of this page
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110
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111 ---------------------------------------------------
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112
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113 .. class:: infomark
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114
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115 **References**
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116
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117 | Thevenot EA., Roux A., Xu Y., Ezan E., and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335 (http://dx.doi.org/10.1021/acs.jproteome.5b00354)
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118 | Mason R., Tracy N. and Young J. (1997). A practical approach for interpreting multivariate T2 control chart signals. *Journal of Quality Technology*, **29**:396-406.
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119 | Alonso A., Julia A., Beltran A., Vinaixa M., Diaz M., Ibanez L., Correig X. and Marsal S. (2011). AStream: an R package for annotating LC/MS metabolomic data. *Bioinformatics*, **27**:1339-1340. (http://dx.doi.org/10.1093/bioinformatics/btr138)
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120
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121 ---------------------------------------------------
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122
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123 ========================
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124 Quality Metrics
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125 ========================
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126
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127 -----------
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128 Description
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129 -----------
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130
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131 | The **Quality Metrics** tool provides quality metrics of the samples and variables, and visualization of the data matrix
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132 | The optional *Coefficient of Variation* arguments allows to flag the variables with a pool CV (or a pool CV over sample CV ratio) above a specific threshold
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133 | The advanced *PoolAsPool1* argument is used when correlations with pool dilutions are computed: When set to TRUE [default], samples indicated as "pool" will be considered as "pool1" for the correlation together with the other pool dilutions (e.g. "pool2", "pool4", etc.); otherwise, "pool" samples will not be considered to compute the correlation (this enables the experimenter to have distinct "pool" samples for the computation of CV and "pool1" samples for the computation of dilution)
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134 | The **sampleMetadata** is returned as output with 3 additional columns containing the p-values for the Hotellings'T2 and Z-scores of intensity deciles and proportion of missing values
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135 | The **variableMetadata** is returned as output; in case a **sampleType** column is included in the input sampleMetadata file, additional columns will be added to indicate the variable quality metrics (eg mean, sd, CV on 'pool', 'sample' or 'blank', or correlation with pool dilutions, depending on the known type present in the 'sampleType' column)
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136 | A **figure** is generated (pdf file) which illustrates the main computed sample and variable metric values
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137
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138
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139
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140 -----------------
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141 Workflow position
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142 -----------------
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143
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144 .. image:: QualityControl.png
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145 :width: 800
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146
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147
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148
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149 -----------
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150 Input files
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151 -----------
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152
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153 +----------------------------+---------+
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154 | Parameter : num + label | Format |
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155 +============================+=========+
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156 | 1 : Data matrix file | tabular |
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157 +----------------------------+---------+
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158 | 2 : Sample metadata file | tabular |
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159 +----------------------------+---------+
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160 | 3 : Variable metadata file | tabular |
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161 +----------------------------+---------+
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162
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163 ----------
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164 Parameters
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165 ----------
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166
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167 Data matrix
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168 | contains the intensity values of the variables.
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169 |
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170
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171 Sample metadata file
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172 | contains the metadata of the samples; in particular
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173 | when the 'sampleType' column is available, with known types such as 'blank', 'sample', 'pool', 'poolN' (where N is a dilution factor of the pool), metrics will be computed (eg mean, sd, CV, correlation with the dilution factor, etc) for each variable (see the 'PoolAsPool1' argument below)
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174 | 'pool' (and 'sample') should be present in the 'sampleType' column when setting the 'coefficient of variation' to TRUE
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175 |
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176
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177 Variable metadata file
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178 | contains variable information.
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179 |
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180
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181 Note:
2
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182 | **Required formats** for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org (http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToFormatDataForPostprocessing_v02.pdf)
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183 | The formats of the 3 tables can be further checked with the **Check Format** module
0
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184 |
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185
2
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186
0
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187 Coefficient of Variation
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188 | If 'yes' (not default): variables are classed according to the Coefficient of Variation (CV)
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189 | i.e.: CV of pools (and CV of samples if needed) are calculated and compared to a defined threshold;
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190 | then variables are classed with a 0/1 coding.
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191 |
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192
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193 Which type of CV calculation should be done (only if CV=yes)
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194 | Type of CV comparison that will be used.
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195 | 'ratio between pool and sample CVs' **OR** 'only pool CV'
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196 |
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197
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198 Threshold (only if CV=yes)
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199 | If comparing pool and sample CVs, corresponds to the max ratio tolerated (basically between 1.0 and 1.25).
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200 | Else corresponds to the max pool CV tolerated (basically 0.3).
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201 |
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202
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203 PoolAsPool1 (Advanced parameter)
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204 | If 'poolN' (where N is a dilution factor) sample types are present in the 'sampleType' column of the sample metadata file, the Pearson correlation of the intensity with the dilution factor is computed for each variable; the 'PoolAsPool1' parameter indicates whether samples of 'pool' types should be considered as 'pool1' (and hence included in the computation of dilution correlations); default is TRUE
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205
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206
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207 ------------
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208 Output files
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209 ------------
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210
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211
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212 sampleMetadata.tabular
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213 | tsv output
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214 | 3 additional columns have been added to the input sampleMetadata file and contain the **p-values** of
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215 | 1) the **Hotelling's T2** test in the first plane of PC components (Mason et al, 1997)
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216 | 2) the **Z-score** of **intensity deciles** (Alonso et al, 2011)
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217 | 3) the **Z-score** of the proportion of **missing values** (Alonso et al, 2011)
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218 | for each test, low p-values indicate samples with extreme behaviour
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219 |
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220
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221 variableMetadata.tabular
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222 | tsv output
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223 | When the type of samples is available (ie the **sampleType** column is included in the input sampleMetadata file), variable metrics are computed: **sample**, **pool**, and **blank** **mean**, **sd** and **CV** (if the corresponding types are present in the 'sampleType' column), as well as **'blank' mean / 'sample' mean**, and **'pool' CV / 'sample' CV ratio**
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224 | If pool dilutions have been used and are indicated in the 'sampleType' column as **poolN** where N is an integer indicating the dilution factor (eg **pool2** for a two-fold dilution of the pool; note that the non-diluted pool remains indicated as 'pool') the Pearson **correlation** (and corresponding p-value) between the intensity and the dilution factor is computed for each variable.
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225 | When the **Coefficient of variation** argument is set to 'TRUE', the variableMetadata begins with 2 (or 3) columns indicating the pool CV (and the sample CV) and if the pool CV (or the ratio between pool CV and sample CV) is above the selected threshold
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226 |
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227
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228 figure.pdf
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229 | Figure summarizing the various values of the computed metrics and tests; includes several visualizations of the samples (eg, PCA scores) and intensities (eg, image of the data matrix)
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230 |
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231
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232 information.txt
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233 | Text file with informations regarding the metrics computed, eg those depending on the availability of the 'sampleMetadata' column, and specific types such as 'sample', 'pool', pool dilutions ('poolN'), or 'blank'
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234 |
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235
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236
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237 ---------------------------------------------------
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238
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239 ---------------
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240 Working example
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241 ---------------
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242
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243 |
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244
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245 .. class:: infomark
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246
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247 See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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248
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249 ---------------------------------------------------
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250
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251 ----
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252 NEWS
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253 ----
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254
2
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255 CHANGES IN VERSION 2.2.8
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256 ========================
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257
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258 MINOR MODIFICATION
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259
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260 In the case of a distinct sample order between dataMatrix and sampleMetadata, the sample order from the dataMatrix is matched to sampleMetadata internally for the computations and graphics without modifying the order in the sampleMetadata output (a warning is generated in the information file); to get the re-ordered dataMatrix as output, please use the Check Format module
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261
1
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262 CHANGES IN VERSION 2.2.6
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263 ========================
2
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264
1
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265 MINOR MODIFICATION
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266
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267 Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value)
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268
0
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269 CHANGES IN VERSION 2.2.4
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270 ========================
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271
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272 Additional running and installation tests added with planemo, conda, and travis
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273
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274 CHANGES IN VERSION 2.2.3
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275 ========================
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276
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277 INTERNAL MODIFICATIONS
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278
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279 Modifications of the **qualitymetrics_script.R** file to handle the recent **ropls** package versions (i.e. 1.3.15 and above) which use S4 classes
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280
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281 Creating tests for the R code
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282
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283 CHANGES IN VERSION 2.2.2
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284 ========================
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285
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286 Minor internal changes
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287
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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288
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289 </help>
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290
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291 <citations>
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292 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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293 <citation type="doi">10.1093/bioinformatics/btr138</citation>
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294 <citation type="bibtex">@Article{Mason1997,
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295 Title = {A practical approach for interpreting multivariate T2 control chart signals},
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296 Author = {Mason, RL. and Tracy, ND. and Young, JC.},
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297 Journal = {Journal of Quality Technology},
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298 Year = {1997},
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299 Number = {4},
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300 Pages = {396-406},
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301 Volume = {29},
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302 }</citation>
2
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303 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
0
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304 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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305 </citations>
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306
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307 </tool>