Mercurial > repos > ethevenot > multivariate
annotate multivariate_config.xml @ 1:da272496b32d draft
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
author | ethevenot |
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date | Sat, 30 Jul 2016 12:31:20 -0400 |
parents | fafba524dca6 |
children | fa173e12e185 |
rev | line source |
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1
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
ethevenot
parents:
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1 <tool id="Multivariate" name="Multivariate" version="2.3.4"> |
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fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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2 <description>PCA, PLS and OPLS</description> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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3 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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4 <requirements> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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5 <requirement type="package" version="3.2.2">R</requirement> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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6 <requirement type="package">r-batch</requirement> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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7 <requirement type="package" version="1.4.2">bioconductor-ropls</requirement> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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8 </requirements> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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9 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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10 <command><![CDATA[ |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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11 $__tool_directory__/multivariate_wrapper.R |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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12 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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13 dataMatrix_in "$dataMatrix_in" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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14 sampleMetadata_in "$sampleMetadata_in" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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15 variableMetadata_in "$variableMetadata_in" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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16 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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17 respC "$respC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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18 predI "$predI" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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19 orthoI "$orthoI" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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20 testL "$testL" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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21 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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22 #if $advGph.opgC == "full" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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23 typeC "$advGph.typeC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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24 parAsColC "$advGph.parAsColC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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25 parCexN "$advGph.parCexN" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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26 parPc1I "$advGph.parPc1I" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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27 parPc2I "$advGph.parPc2I" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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28 parMahalC "$advGph.parMahalC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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29 parLabVc "$advGph.parLabVc" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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30 #end if |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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31 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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32 #if $advCpt.opcC == "full" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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33 algoC "$advCpt.algoC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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34 crossvalI "$advCpt.crossvalI" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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35 log10L "$advCpt.log10L" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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36 permI "$advCpt.permI" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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37 scaleC "$advCpt.scaleC" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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38 #end if |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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39 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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40 sampleMetadata_out "$sampleMetadata_out" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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41 variableMetadata_out "$variableMetadata_out" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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42 figure "$figure" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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43 information "$information" |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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44 ]]></command> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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45 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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46 <inputs> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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47 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" /> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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48 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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49 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata, decimal: '.', missing: NA, mode: character and numerical, sep: tabular" /> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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50 <param name="respC" label="Y Response (for (O)PLS(-DA) only)" type="text" value = "none" help="Notes: 1) PCA: keep the default (none); 2) (O)PLS(-DA): indicate the name of the column of the sample table to be modeled" /> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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51 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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52 <param name="predI" label="Number of predictive components" type="select" help="Notes: 1) PCA and PLS(-DA): NA can be selected to get a suggestion of the optimal number of predictive components; 2) OPLS(-DA) modeling: select 1 predictive component"> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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53 <option value="NA" selected="true">NA</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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54 <option value="1">1</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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55 <option value="2">2</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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56 <option value="3">3</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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57 <option value="4">4</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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58 <option value="5">5</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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59 <option value="6">6</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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60 <option value="7">7</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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61 <option value="8">8</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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62 <option value="9">9</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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63 <option value="10">10</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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64 </param> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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65 <param name="orthoI" label="Number of orthogonal components (for OPLS(-DA) only)" type="select" help="Notes: 1) PCA and PLS(-DA): keep the default value (0); 2) OPLS(-DA): NA can be selected to get a suggestion of the optimal number of orthogonal components"> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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66 <option value="0">0</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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67 <option value="NA">NA</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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68 <option value="1">1</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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69 <option value="2">2</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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70 <option value="3">3</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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71 <option value="4">4</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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72 <option value="5">5</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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73 <option value="6">6</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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74 <option value="7">7</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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75 <option value="8">8</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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76 <option value="9">9</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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77 <option value="10">10</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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78 </param> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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79 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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80 <param name="testL" label="Samples to be tested" type="select" help="In case predictions should be computed on test samples, provide in your sampleMetadata a column named test. (use exactly this column name, with the dot at the end) and containing yes and no values to indicate which samples should be tested; for those samples, the values of the response will not be used (you can leave NA in the response column of the sample metadata)"> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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81 <option value="TRUE">yes</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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82 <option value="FALSE" selected="true">no</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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83 </param> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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84 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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85 <conditional name="advGph"> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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86 <param name="opgC" type="select" label="Advanced graphical parameters" > |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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87 <option value="default" selected="true">Use default</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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88 <option value="full">Full parameter list</option> |
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89 </param> |
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90 |
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91 <when value="default"/> |
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92 <when value="full"> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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93 <param name="typeC" label="Graphic type" type="select" help=""> |
fafba524dca6
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94 <option value="correlation">correlation</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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95 <option value="outlier">outlier</option> |
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96 <option value="overview">overview</option> |
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97 <option value="permutation">permutation</option> |
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98 <option value="predict-train">predict-train</option> |
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99 <option value="summary" selected="true">summary</option> |
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100 <option value="x-loading">x-loading</option> |
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101 <option value="x-score">x-score</option> |
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102 <option value="x-variance">x-variance</option> |
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103 <option value="xy-score">xy-score</option> |
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104 <option value="xy-weight">xy-weight</option> |
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105 </param> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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106 <param name="parMahalC" label="Ellipses" type="text" value = "NA" help="Name of the sample metadata column with the classes to be used for drawing ellipses; for (O)PLS-DA, the default 'NA' means that the same name as the 'Response' argument above will be used; if you do not want ellipses, use none instead of NA" /> |
fafba524dca6
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107 <param name="parAsColC" label="Sample colors" type="text" value = "none" help="Indicate the name of the sample metadata column with the names to be converted into colors; by default (none), data matrix sample names will be used" /> |
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108 <param name="parLabVc" label="Sample labels" type="text" value = "none" help="Indicate the name of the sample metadata column with the names to be used as labels; By default (none), sample names from the data matrix will be used" /> |
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109 <param name="parPc1I" label="Component to be displayed as abscissa" type="select" value = "-" help="In case of OPLS(-DA), the first component (i.e. the predictive component) must be set to 1"> |
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110 <option value="1">1</option> |
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111 <option value="2">2</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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112 <option value="3">3</option> |
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113 <option value="4">4</option> |
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114 <option value="5">5</option> |
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115 <option value="6">6</option> |
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116 <option value="7">7</option> |
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117 <option value="8">8</option> |
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118 <option value="9">9</option> |
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119 <option value="10">10</option> |
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120 </param> |
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121 <param name="parPc2I" label="Component to be displayed as ordinate" type="select" help="In case of OPLS(-DA), the orthogonal component of the selected value - 1 will be displayed (e.g. to see the first orthogonal component, select the value '2' below)"> |
fafba524dca6
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122 <option value="2">2</option> |
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123 <option value="3">3</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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124 <option value="4">4</option> |
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125 <option value="5">5</option> |
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126 <option value="6">6</option> |
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127 <option value="7">7</option> |
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128 <option value="8">8</option> |
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129 <option value="9">9</option> |
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130 <option value="10">10</option> |
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131 </param> |
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132 <param name="parCexN" type="float" value="0.8" label="Amount by which plotting text should be magnified relative to the default"/> |
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133 |
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134 </when> |
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135 </conditional> |
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136 |
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137 <conditional name="advCpt"> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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138 <param name="opcC" type="select" label="Advanced computational parameters" > |
fafba524dca6
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139 <option value="default" selected="true">Use default</option> |
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140 <option value="full">Full parameter list</option> |
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141 </param> |
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142 |
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143 <when value="default"/> |
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144 <when value="full"> |
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145 <param name="scaleC" label="Scaling" type="select" help="Select 'standard' for mean-centering and unit-variance scaling"> |
fafba524dca6
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146 <option value="standard">standard</option> |
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147 <option value="center">center</option> |
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148 <option value="pareto">pareto</option> |
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149 </param> |
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150 <param name="permI" label="Permutation testing for (O)PLS(-DA): Number of permutations" type="select" help="Default is 20 for single response models without train/test partition, and 0 otherwise"> |
fafba524dca6
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151 <option value="0">0</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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152 <option value="20" selected="true">20</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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153 <option value="100">100</option> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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154 <option value="1000">1000</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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155 </param> |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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156 <param name="log10L" label="Log10 transformation" type="select" help=""> |
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157 <option value="TRUE">yes</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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158 <option value="FALSE" selected="true">no</option> |
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159 </param> |
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160 <param name="algoC" label="Algorithm" type="select" help="Default algorithm is 'svd' for PCA and 'nipals' for PLS and OPLS; when performing PCA with 'svd' on an data matrix containing missing values, NAs are set to half the minimum of non-missing values and a warning is generated; an alternative is to use the 'nipals' algorithm (able to handle a moderate amount of missing values)"> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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161 <option value="default">default</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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162 <option value="nipals">nipals</option> |
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163 <option value="svd">svd</option> |
fafba524dca6
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164 </param> |
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165 <param name="crossvalI" label="Number of cross-validation segments" type="select" help="Must be less than or equal to the number of samples"> |
fafba524dca6
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166 <option value="1">1</option> |
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167 <option value="2">2</option> |
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168 <option value="3">3</option> |
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169 <option value="4">4</option> |
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170 <option value="5">5</option> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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171 <option value="6">6</option> |
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172 <option value="7" selected="true">7</option> |
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173 <option value="8">8</option> |
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174 <option value="9">9</option> |
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175 <option value="10">10</option> |
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176 </param> |
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177 |
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178 </when> |
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179 </conditional> |
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180 |
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181 </inputs> |
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182 |
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183 <outputs> |
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184 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> |
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185 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> |
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186 <data name="figure" label="${tool.name}__figure.pdf" format="pdf"/> |
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187 <data name="information" label="${tool.name}__information.txt" format="txt"/> |
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188 </outputs> |
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189 |
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190 <tests> |
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191 <test> |
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192 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/> |
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193 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/> |
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194 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/> |
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195 <param name="respC" value="age"/> |
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196 <param name="predI" value="1"/> |
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197 <param name="orthoI" value="1"/> |
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198 <param name="testL" value="FALSE"/> |
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199 <output name="sampleMetadata_out"> |
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200 <assert_contents> |
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201 <has_n_columns n="9"/> |
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202 </assert_contents> |
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203 </output> |
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204 <output name="variableMetadata_out"> |
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205 <assert_contents> |
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206 <has_n_columns n="7"/> |
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207 </assert_contents> |
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208 </output> |
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209 </test> |
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210 </tests> |
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211 |
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212 <help> |
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213 |
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214 .. class:: infomark |
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215 |
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216 **Author** Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr) |
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217 |
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218 --------------------------------------------------- |
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219 |
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220 .. class:: infomark |
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221 |
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222 **Please cite** |
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223 |
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224 Etienne A. Thevenot, Aurelie Roux, Ying Xu, Eric Ezan, and Christophe Junot (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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225 |
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226 --------------------------------------------------- |
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227 |
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228 .. class:: infomark |
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229 |
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230 **R package** |
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231 |
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232 The *ropls* package is available from the bioconductor repository (http://bioconductor.org/packages/ropls). |
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233 |
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234 --------------------------------------------------- |
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235 |
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236 .. class:: infomark |
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237 |
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238 **Tool updates** |
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239 |
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240 See the **NEWS** section at the bottom of this page |
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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 Multivariate analysis with PCA and (O)PLS(-DA) |
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246 ============================================== |
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247 |
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248 ----------- |
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249 Description |
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250 ----------- |
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251 |
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252 **Latent variable modeling** with Principal Component Analysis (**PCA**) and Partial Least Squares (**PLS**) are powerful methods for **visualization**, **regression**, **classification**, and feature selection of **omics data** where the number of variables exceeds the number of samples and with multicollinearity among variables (Wold et al, 2001; Thenenhaus, 1998; Wehrens, 2011; Eriksson et al, 2006; Trygg et al, 2007). Orthogonal Partial Least Squares (**OPLS**) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation (Trygg and Wold, 2002). While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to **scores**, **loadings** and **weights** plots, the module provides metrics and graphics to determine the optimal number of components (e.g. with the **R2** and **Q2** coefficients; Wold et al, 2001; Thenenhaus, 1998; Eriksson et al, 2006), check the **validity of the model** by permutation testing (Szymanska et al, 2012), detect **outliers** (Wold et al, 2001; Thenenhaus, 1998; Hubert et al, 2005), and provide several metrics to assess the importance of the variables in the model (e.g. **Variable Importance in Projection** or regression coefficients; Wold et al, 2001; Mehmood et al, 2012; Galindo-Prieto et al, 2014). The module is an implementation of the **ropls** R package available from Bioconductor (Thevenot et al, 2015). |
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253 |
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254 -------- |
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255 Comments |
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256 -------- |
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257 |
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258 1) Overfitting |
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259 | Overfitting (i.e., building a model with good performances on the training set but poor performances on a new test set) is a major caveat of machine learning techniques applied to data sets with more variables than samples. A simple simulation with a random dataMatrix and a random response shows that perfect PLS-DA classification can be achieved as soon as the number of variables exceeds the number of samples (Wehrens, 2011). It is therefore essential to check that the Q2 value of the model is significant by random permutation of the labels: the number of permutations (advanced computational parameter) is set to 20 by default but should be increased for confirmation of the results. |
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260 |
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261 2) VIP from OPLS models |
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262 | The classical VIP metric is not useful for OPLS modeling of a single response since (Galindo-Prieto et al, 2014; Thevenot et al, 2015). In fact, when features are standardized, we can demonstrate a mathematical relationship between VIP and *p*-values from a Pearson correlation test (Thevenot et al, 2015): classical VIP are therefore univariate for OPLS(-DA) models (and identical whatever the number of orthogonal components of the model). |
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263 | Galindo-Prieto et al. (2014) have therefore recently suggested new VIP metrics for OPLS, VIP*pred* and VIP*ortho*, to separately measure the influence of the features in the modeling of the dispersion correlated to, and orthogonal to the response, respectively. |
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264 | For OPLS(-DA) models, the output variableMetadata contains the 2 metrics: VIP_pred is a measure of the variable importance in prediction and VIP_ortho is a measure of the variable importance in orthogonal modeling. VIP_pred and VIP_ortho are scaled as the classical VIP (i.e., the mean of their squared values equals 1). |
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265 |
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266 3) (Orthogonal) Partial Least Squares Discriminant Analysis: (O)PLS-DA |
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267 | The approach for discriminant analysis implemented in the module relies on internal conversion of the response into a dummy vector (resp. a matrix when the number of classes is > 2), mean-centering and unit-variance scaling of the vector (resp. the matrix), and PLS (resp. PLS2) regression modeling. |
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268 | When the sizes of the 2 classes are unbalanced, Brereton and Lloyd (2014) have demonstrated that a bias is introduced in the computation of the decision rule, which penalizes the class with the highest size. In the multiclass case, the proportions of 0 and 1 in the columns is usually unbalanced (even in the case of balanced size of the classes) resulting in a bias (Brereton and Llyod, 2014). |
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269 | With the current implementation of the module, we thus recommend to stick to binary discrimination and use balanced classes for optimal use. |
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270 |
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271 ---------- |
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272 References |
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273 ---------- |
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274 |
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275 | Brereton R.G. and Lloyd G.R. (2014). Partial least squares discriminant analysis: taking the magic away. *Journal of Chemometrics*, 28:213-225. http://dx.doi.org/10.1002/cem.2609 |
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276 | Eriksson I., Johansson E., Kettaneh-Wold N. and Wold S. (2001). Multi- and megavariate data analysis. Principles and applications. *Umetrics Academy*. |
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277 | Galindo-Prieto B., Eriksson L. and Trygg J. (2014). Variable influence on projection (VIP) for orthogonal projections to latent structures (OPLS). *Journal of Chemometrics*, 28:623-632. http://dx.doi.org/10.1002/cem.2627 |
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278 | Hubert M., Rousseeuw P. and Vanden Branden K. (2005). ROBPCA: a new approach to robust principal component analysis. *Technometrics*, 47:64-79. http://dx.doi.org/10.1198/004017004000000563 |
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279 | Mehmood T., Liland K.H., Snipen L. and Saebo S. (2012). A review of variable selection methods in Partial Least Squares Regression. *Chemometrics and Intelligent Laboratory Systems*, 118:62-69. http://dx.doi.org/10.1016/j.chemolab.2012.07.010 |
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280 | Szymanska E., Saccenti E., Smilde A. and Westerhuis J. (2012). Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies. *Metabolomics*, 8:3-16. http://dx.doi.org/10.1007/s11306-011-0330-3 |
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281 | Tenenhaus M. (1998). La regression PLS : theorie et pratique. *Technip*. |
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282 | Thevenot E.A., 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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283 | Trygg J. and Wold S. (2002). Orthogonal projection to latent structures (O-PLS). *Journal of Chemometrics*, 16:119-128. http://dx.doi.org/10.1002/cem.695 |
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284 | Trygg J., Holmes E. and Lundstedt T. (2007). Chemometrics in Metabonomics. *Journal of Proteome Research*, 6:469-479. http://dx.doi.org/10.1021/pr060594q |
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285 | Wehrens W. (2011). Chemometrics with R. *Springer*. |
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286 | Wold S., Sjostrom M. and Eriksson L. (2001). PLS-regression: a basic tool of chemometrics. *Chemometrics and Intelligent Laboratory Systems*, 58:109-130. http://dx.doi.org/10.1016/S0169-7439(01)00155-1 |
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287 |
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288 ----------------- |
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289 Workflow position |
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290 ----------------- |
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291 |
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292 .. image:: multivariate_workflowPositionImage.png |
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293 :width: 600 |
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294 |
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295 ----------- |
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296 Input files |
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297 ----------- |
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298 |
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299 +---------------------------+------------+ |
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300 | File | Format | |
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301 +===========================+============+ |
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302 | 1) Data matrix | tabular | |
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303 +---------------------------+------------+ |
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304 | 2) Sample metadata | tabular | |
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305 +---------------------------+------------+ |
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306 | 3) Variable metadata | tabular | |
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307 +---------------------------+------------+ |
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308 |
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309 |
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310 ---------- |
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311 Parameters |
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312 ---------- |
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313 |
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314 Data matrix file |
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315 | variable x sample **dataMatrix** tabular separated file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below) |
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316 | |
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317 |
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318 Sample metadata file |
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319 | sample x metadata **sampleMetadata** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values |
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320 | |
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321 |
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322 Variable metadata file |
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323 | variable x metadata **variableMetadata** tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values |
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324 | |
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325 |
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326 Y Response (mandatory for PLS and OPLS; keep the default, none, for PCA) |
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327 | Column of the sample metadata table to be used as (qualitative or quantitative) response for (O)PLS(-DA) |
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328 | |
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329 |
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330 Number of (predictive) components (default = NA) |
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331 | For OPLS(-DA), this number is automatically converted to 1; otherwise if set to **NA**, the optimal number of components is automatically determined by cross-validation: components are extracted until (i) PCA case: the variance is less than the mean variance of all components (note that this rule requires all components to be computed and can be quite time-consuming for large datasets) or (ii) PLS case: either R2Y of the component is less than 0.01 or Q2Y is less than 0 (when the dataset contains more than 100 samples) or 0.05 otherwise |
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332 | |
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333 |
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334 Number of orthogonal components (mandatory for OPLS(-DA); default = 0 otherwise) |
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335 | When set to **0** [default], PLS will be performed; otherwise OPLS will be peformed; when set to **NA**, OPLS is performed and the number of orthogonal components is automatically computed by using cross-validation |
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336 | |
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337 |
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338 Samples for prediction (for (O)PLS(-DA) only; default is no) |
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339 | In case predictions should be computed on test samples, provide in your **sampleMetadata** a column named **test.** (use exactly this column name, with the dot at the end) and containing **yes** and **no** values to indicate which samples should be tested; for those samples, the values of the response will not be used (you can leave **NA** in the response column of the **sampleMetadata**) |
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340 | |
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341 |
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342 Advanced graphical parameters |
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343 | |
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344 |
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345 Graphic type (default = summary) |
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346 | **summary** 4-plot graphics showing **overview** (or **permutation** when the number of permutations is superior to 0; see below), **outlier**, **x-loading** and **x-score** |
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347 | **correlation** Variable correlations with the components |
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348 | **outlier** Observation diagnostics (score and orthogonal distances) |
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349 | **overview** Model overview showing R2Ycum and Q2cum (or 'Variance explained' for PCA) |
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350 | **permutation** Scatterplot of R2Y and Q2Y actual and simulated models after random permutation of response values |
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351 | **predict-train** Predicted vs Actual Y for the reference set (only if Y has a single column) |
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352 | **x-loading** X-Loadings |
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353 | **x-score** X-Scores |
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354 | **x-varcor** Spread of raw variables corresp. to quantile variances and, if the number of variables is less than 100, correlations between the X-variables |
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355 | **xy-score** XY-Scores, |
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356 | **xy-weight** XY-Weights |
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357 | .pdf image files can be converted to high-resolution .tif images (e.g. for publication) by using in the open-source Gimp software: open the .pdf with resolution = 300, and export as a .tif image without compression |
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358 | |
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359 |
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360 Ellipses (default = NA) |
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361 | If 'NA' ellipses are drawn automatically for (O)PLS-DA, or for PCA, when a column of characters is selected in the 'sample colors' argument below. If you do not want ellipses, set to none. |
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362 | |
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363 |
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364 Sample colors (default = none) |
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365 | Name of the column of the sample table with the classes to be used for coloring the samples on plots (e.g. for PCA or if you wish to highlight a factor distinct from the response above); by default (none) sample names are converted into a color palette" |
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366 | |
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367 |
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368 Sample labels (default = none) |
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369 | Name of the column of the sample table with the classes to be used for labeling the samples on plots; by default (none), sample names will be used |
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370 | |
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371 |
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372 Component to be displayed as abscissa (default = 1) |
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373 | In case of OPLS(-DA), the first component (i.e. the predictive component) must be set to 1" |
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374 | |
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375 |
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376 Component to be displayed as ordinate (default = 2) |
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377 | Note: In case of OPLS(-DA), the orthogonal component of the value below - 1 will be displayed (e.g. to see the first orthogonal component, select the value **2** (default) |
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378 | |
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379 |
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380 Number of variables most contributing to loadings to be highlighted (default = 3) |
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381 | Such variables will be colored in red on the loading plot; In addition, the loading values and the correlation with the components will be printed in the text summary |
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382 | |
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383 |
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384 Advanced computational parameters |
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385 | |
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386 |
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387 Scaling (default = standard) |
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388 | Either mean-centering alone (**center**), or followed by pareto scaling (**pareto**), or unit-variance scaling (**standard**) |
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389 | |
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390 |
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391 Permutation testing for (O)PLS(-DA) models: Number of permutations (default = 20) |
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392 | Number of random permutations of response labels to estimate R2Y and Q2Y significance; Default is 10 for single response models and 0 otherwise |
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393 | |
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394 |
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395 Log10 transformation (default = no) |
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396 | Should the data matrix values be log10 transformed? Note: zeros are set to 1 prior to transformation |
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397 | |
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398 |
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399 Train/test partition (default = none) |
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400 | When set to **odd**, samples with odd indices are used to train the model, which is subsequently tested on the samples with even indices; a RMSEP (root mean square error estimation of prediction) is computed, in addition to the RMSEE (error of estimation). Note that in case of a qualitative response, the proportion of samples in each class in the full dataset is preserved within the reference and train subsets |
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401 | |
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402 |
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403 Algorithm (default = svd for PCA and nipals for PLS and OPLS) |
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404 | When using **svd** (singular value decomposition) for PCA on an **dataMatrix** containing missing values (NA), the latters are set to half the minimum of non-missing values and a warning is generated; an alternative is to use the **nipals** algorithm (non-linear iterative partial least squares, based on a power method to find eigenvalues, and able to handle a small amount of missing values); For PLS and OPLS, only the **nipals** algorithm is available |
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405 | |
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406 |
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407 Number of cross-validation segments (default = 7) |
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408 | |
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409 |
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410 |
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411 ------------ |
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412 Output files |
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413 ------------ |
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414 |
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415 |
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416 sampleMetadata_out.tabular |
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417 | **sampleMetadata** file identical to the file given as argument, except that two columns with the x-scores of the displayed components have been added |
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418 | |
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419 |
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420 variableMetadata_out.tabular |
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421 | **variableMetadata** file identical to the file given as argument, except that i) 3 columns with the x-loadings of the displayed components, and the regression coefficients, have been added, ii) in the case of PLS, a column with the VIP values (variable importance in projection of the model with all components) has been added, iii) in the case of OPLS, 2 columns with the VIP_pred and VIP_ortho have been added. |
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422 | |
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423 |
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424 figure.pdf |
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425 | Graphic |
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426 | |
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427 |
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428 information.txt |
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429 | Text file with all messages and warnings generated during the computation |
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430 | |
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431 |
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432 --------------------------------------------------- |
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433 |
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434 ---------------- |
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435 Working examples |
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436 ---------------- |
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437 |
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438 | |
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439 |
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440 .. class:: infomark |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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441 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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442 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2** or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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443 |
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444 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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445 Figure output |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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446 ============= |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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447 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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448 .. image:: multivariate_workingExampleImage.png |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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449 :width: 600 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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450 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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451 --------------------------------------------------- |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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452 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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453 ---- |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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454 NEWS |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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455 ---- |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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456 |
1
da272496b32d
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457 CHANGES IN VERSION 2.3.4 |
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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458 ======================== |
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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459 |
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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460 INTERNAL MODIFICATIONS |
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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461 |
da272496b32d
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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462 Minor update in .shed.yml file |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit dbdc8c3e17ea6ef7139e77cbb6130de949ea2a05
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463 |
0
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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464 CHANGES IN VERSION 2.3.2 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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465 ======================== |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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466 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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467 NEW FEATURES |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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468 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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469 Error messages are generated in OPLS(-DA) models in case of non-significance of either the predictive or the first orthogonal component |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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470 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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471 INTERNAL MODIFICATIONS |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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472 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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473 Modifications of the **wrapper** file to handle the recent **ropls** package versions (i.e. 1.3.15 and above) which use S4 classes |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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474 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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475 CHANGES IN VERSION 2.3.0 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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476 ======================== |
fafba524dca6
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|
477 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
478 NEW FEATURES |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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479 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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480 1) **Predictions** now available (see the 'Samples to be tested' argument) |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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481 2) OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section) |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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482 3) **Multiclass PLS-DA** implemented (see the 'comments' section) |
fafba524dca6
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483 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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484 MINOR MODIFICATIONS |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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485 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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486 1) Changes in color palette: black/grey colors for diagnostics and other colors for scores |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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487 2) Default number of permutations set to 20 (instead of 10) |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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488 3) Predictive components denoted in the tables by 'p' (instead of 'h' previously) |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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489 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
490 CHANGES IN VERSION 2.2.4 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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491 ======================== |
fafba524dca6
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492 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
493 1) Correction in the Galaxy wrapper (in the previous version, the number of predictive components was sometimes set to the maximum by mistake) |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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494 2) The regression coefficients are now provided as a new column of the variableMetadata output |
fafba524dca6
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495 |
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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
496 CHANGES IN VERSION 2.2.3 |
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497 ======================== |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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498 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
499 The default number of permutations is set to 10 (instead of 100) as a compromise to enable both a quick computation and a first hint at model significance |
fafba524dca6
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500 |
fafba524dca6
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|
501 CHANGES IN VERSION 2.2.2 |
fafba524dca6
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502 ======================== |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
503 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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|
504 1) A default of 100 permutations has been set in order to check for overfitting; in addition, 'permutation', 'overview', and 'outlier' plots are now displayed by default |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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505 2) Classification is currently implemented for two-class responses only |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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506 3) *dataMatrix* is not modified by the tool, so it does not appear as an output files |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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507 4) Double cross-validation (advanced computational parameters): 'odd' now refers to train (instead to test) indices |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
508 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
509 </help> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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510 |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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|
511 <citations/> |
fafba524dca6
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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512 </tool> |