multivariate: multivariate_config.xml annotate

annotate multivariate_config.xml @ 1:60c360e466a8 draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3

author	ethevenot
date	Wed, 28 Feb 2018 10:04:14 -0500
parents	4b9488602d57
children

rev	line source
0 4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	1 <tool id="Multivariate" name="Multivariate" version="2.3.10">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	2 <description>PCA, PLS and OPLS</description>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	3
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	4 <requirements>
1 60c360e466a8 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3 ethevenot parents: 0 diff changeset	5 <requirement type="package" version="1.1_4">r-batch</requirement>
60c360e466a8 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3 ethevenot parents: 0 diff changeset	6 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>
0 4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	7 </requirements>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	8
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	9 <stdio>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	10 <exit_code range="1:" level="fatal" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	11 </stdio>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	12
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	13 <command><![CDATA[
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	14 Rscript $__tool_directory__/multivariate_wrapper.R
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	15
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	16 dataMatrix_in "$dataMatrix_in"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	17 sampleMetadata_in "$sampleMetadata_in"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	18 variableMetadata_in "$variableMetadata_in"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	19
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	20 respC "$respC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	21 predI "$predI"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	22 orthoI "$orthoI"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	23 testL "$testL"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	24
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	25 #if $advGph.opgC == "full"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	26 typeC "$advGph.typeC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	27 parAsColC "$advGph.parAsColC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	28 parCexN "$advGph.parCexN"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	29 parPc1I "$advGph.parPc1I"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	30 parPc2I "$advGph.parPc2I"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	31 parMahalC "$advGph.parMahalC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	32 parLabVc "$advGph.parLabVc"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	33 #end if
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	34
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	35 #if $advCpt.opcC == "full"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	36 algoC "$advCpt.algoC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	37 crossvalI "$advCpt.crossvalI"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	38 log10L "$advCpt.log10L"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	39 permI "$advCpt.permI"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	40 scaleC "$advCpt.scaleC"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	41 #end if
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	42
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	43 sampleMetadata_out "$sampleMetadata_out"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	44 variableMetadata_out "$variableMetadata_out"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	45 figure "$figure"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	46 information "$information"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	47
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	48 #if $save_rdata:
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	49 ropls_out "$ropls_out"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	50 #end if
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	51 ]]></command>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	52
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	53 <inputs>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	54 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, sep: tabular" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	55 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	56 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	57 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	58
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	59 <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">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	60 <option value="NA" selected="true">NA</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	61 <option value="1">1</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	62 <option value="2">2</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	63 <option value="3">3</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	64 <option value="4">4</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	65 <option value="5">5</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	66 <option value="6">6</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	67 <option value="7">7</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	68 <option value="8">8</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	69 <option value="9">9</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	70 <option value="10">10</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	71 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	72 <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">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	73 <option value="0">0</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	74 <option value="NA">NA</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	75 <option value="1">1</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	76 <option value="2">2</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	77 <option value="3">3</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	78 <option value="4">4</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	79 <option value="5">5</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	80 <option value="6">6</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	81 <option value="7">7</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	82 <option value="8">8</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	83 <option value="9">9</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	84 <option value="10">10</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	85 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	86
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	87 <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)">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	88 <option value="TRUE">yes</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	89 <option value="FALSE" selected="true">no</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	90 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	91
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	92 <conditional name="advGph">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	93 <param name="opgC" type="select" label="Advanced graphical parameters" >
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	94 <option value="default" selected="true">Use default</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	95 <option value="full">Full parameter list</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	96 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	97
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	98 <when value="default"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	99 <when value="full">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	100 <param name="typeC" label="Graphic type" type="select" help="">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	101 <option value="correlation">correlation</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	102 <option value="outlier">outlier</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	103 <option value="overview">overview</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	104 <option value="permutation">permutation</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	105 <option value="predict-train">predict-train</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	106 <option value="summary" selected="true">summary</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	107 <option value="x-loading">x-loading</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	108 <option value="x-score">x-score</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	109 <option value="x-variance">x-variance</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	110 <option value="xy-score">xy-score</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	111 <option value="xy-weight">xy-weight</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	112 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	113 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	114 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	115 <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" />
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	116 <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">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	117 <option value="1">1</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	118 <option value="2">2</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	119 <option value="3">3</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	120 <option value="4">4</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	121 <option value="5">5</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	122 <option value="6">6</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	123 <option value="7">7</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	124 <option value="8">8</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	125 <option value="9">9</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	126 <option value="10">10</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	127 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	128 <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)">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	129 <option value="2">2</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	130 <option value="3">3</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	131 <option value="4">4</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	132 <option value="5">5</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	133 <option value="6">6</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	134 <option value="7">7</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	135 <option value="8">8</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	136 <option value="9">9</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	137 <option value="10">10</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	138 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	139 <param name="parCexN" type="float" value="0.8" label="Amount by which plotting text should be magnified relative to the default"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	140
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	141 </when>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	142 </conditional>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	143
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	144 <conditional name="advCpt">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	145 <param name="opcC" type="select" label="Advanced computational parameters" >
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	146 <option value="default" selected="true">Use default</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	147 <option value="full">Full parameter list</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	148 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	149
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	150 <when value="default"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	151 <when value="full">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	152 <param name="scaleC" label="Scaling" type="select" help="Select 'standard' for mean-centering and unit-variance scaling">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	153 <option value="standard">standard</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	154 <option value="center">center</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	155 <option value="pareto">pareto</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	156 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	157 <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">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	158 <option value="0">0</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	159 <option value="20" selected="true">20</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	160 <option value="100">100</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	161 <option value="1000">1000</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	162 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	163 <param name="log10L" label="Log10 transformation" type="select" help="">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	164 <option value="TRUE">yes</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	165 <option value="FALSE" selected="true">no</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	166 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	167 <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)">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	168 <option value="default">default</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	169 <option value="nipals">nipals</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	170 <option value="svd">svd</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	171 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	172 <param name="crossvalI" label="Number of cross-validation segments" type="select" help="Must be less than or equal to the number of samples">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	173 <option value="1">1</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	174 <option value="2">2</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	175 <option value="3">3</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	176 <option value="4">4</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	177 <option value="5">5</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	178 <option value="6">6</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	179 <option value="7" selected="true">7</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	180 <option value="8">8</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	181 <option value="9">9</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	182 <option value="10">10</option>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	183 </param>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	184
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	185 </when>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	186 </conditional>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	187 <param name="save_rdata" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Save RData in your history"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	188 help="Save the R ropls::opls object in your history for ad hoc analysis and graphing (outside Galaxy, this requires package 'bioconductor-ropls')"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	189 </inputs>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	190
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	191 <outputs>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	192 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	193 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	194 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	195 <data name="information" label="${tool.name}_information.txt" format="txt"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	196 <!-- how would an ropls.rdata datatype be added if that were the desired choice here instead? Specifically, could it be created as part of tool installation? -->
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	197 <data name="ropls_out" label="${tool.name}_${dataMatrix_in.name}.RData" format="rdata">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	198 <filter>save_rdata</filter>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	199 </data>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	200 </outputs>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	201
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	202 <tests>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	203 <test>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	204 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	205 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	206 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	207 <param name="respC" value="age"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	208 <param name="predI" value="1"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	209 <param name="orthoI" value="1"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	210 <param name="testL" value="FALSE"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	211 <output name="sampleMetadata_out">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	212 <assert_contents>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	213 <has_n_columns n="9"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	214 </assert_contents>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	215 </output>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	216 <output name="variableMetadata_out">
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	217 <assert_contents>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	218 <has_n_columns n="7"/>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	219 </assert_contents>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	220 </output>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	221 </test>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	222 </tests>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	223
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	224 <help>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	225
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	226 .. class:: infomark
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	227
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	228 Author Etienne Thevenot (CEA, LIST, MetaboHUB Paris, etienne.thevenot@cea.fr)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	229
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	230 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	231
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	232 .. class:: infomark
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	233
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	234 Please cite
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	235
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	236 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).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	237
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	238 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	239
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	240 .. class:: infomark
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	241
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	242 R package
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	243
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	244 The ropls package is available from the bioconductor repository (http://bioconductor.org/packages/ropls).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	245
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	246 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	247
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	248 .. class:: infomark
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	249
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	250 Tool updates
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	251
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	252 See the NEWS section at the bottom of this page
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	253
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	254 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	255
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	256 ==============================================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	257 Multivariate analysis with PCA and (O)PLS(-DA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	258 ==============================================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	259
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	260 -----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	261 Description
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	262 -----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	263
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	264 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).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	265
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	266 --------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	267 Comments
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	268 --------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	269
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	270 1) Overfitting
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	271 \| 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.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	272
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	273 2) VIP from OPLS models
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	274 \| 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).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	275 \| Galindo-Prieto et al. (2014) have therefore recently suggested new VIP metrics for OPLS, VIPpred and VIPortho, to separately measure the influence of the features in the modeling of the dispersion correlated to, and orthogonal to the response, respectively.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	276 \| 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).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	277
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	278 3) (Orthogonal) Partial Least Squares Discriminant Analysis: (O)PLS-DA
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	279 \| 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.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	280 \| 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).
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	281 \| With the current implementation of the module, we thus recommend to stick to binary discrimination and use balanced classes for optimal use.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	282
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	283 ----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	284 References
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	285 ----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	286
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	287 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	288 \| Eriksson I., Johansson E., Kettaneh-Wold N. and Wold S. (2001). Multi- and megavariate data analysis. Principles and applications. Umetrics Academy.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	289 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	290 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	291 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	292 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	293 \| Tenenhaus M. (1998). La regression PLS : theorie et pratique. Technip.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	294 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	295 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	296 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	297 \| Wehrens W. (2011). Chemometrics with R. Springer.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	298 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	299
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	300 -----------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	301 Workflow position
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	302 -----------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	303
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	304 .. image:: multivariate_workflowPositionImage.png
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	305 :width: 600
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	306
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	307 -----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	308 Input files
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	309 -----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	310
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	311 +---------------------------+------------+
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	312 \| File \| Format \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	313 +===========================+============+
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	314 \| 1) Data matrix \| tabular \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	315 +---------------------------+------------+
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	316 \| 2) Sample metadata \| tabular \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	317 +---------------------------+------------+
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	318 \| 3) Variable metadata \| tabular \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	319 +---------------------------+------------+
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	320
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	321
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	322 ----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	323 Parameters
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	324 ----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	325
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	326 Data matrix file
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	327 \| 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)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	328 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	329
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	330 Sample metadata file
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	331 \| sample x metadata sampleMetadata tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	332 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	333
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	334 Variable metadata file
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	335 \| variable x metadata variableMetadata tabular separated file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	336 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	337
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	338 Y Response (mandatory for PLS and OPLS; keep the default, none, for PCA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	339 \| Column of the sample metadata table to be used as (qualitative or quantitative) response for (O)PLS(-DA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	340 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	341
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	342 Number of (predictive) components (default = NA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	343 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	344 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	345
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	346 Number of orthogonal components (mandatory for OPLS(-DA); default = 0 otherwise)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	347 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	348 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	349
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	350 Samples for prediction (for (O)PLS(-DA) only; default is no)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	351 \| 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)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	352 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	353
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	354 Advanced graphical parameters
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	355 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	356
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	357 Graphic type (default = summary)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	358 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	359 \| correlation Variable correlations with the components
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	360 \| outlier Observation diagnostics (score and orthogonal distances)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	361 \| overview Model overview showing R2Ycum and Q2cum (or 'Variance explained' for PCA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	362 \| permutation Scatterplot of R2Y and Q2Y actual and simulated models after random permutation of response values
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	363 \| predict-train Predicted vs Actual Y for the reference set (only if Y has a single column)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	364 \| x-loading X-Loadings
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	365 \| x-score X-Scores
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	366 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	367 \| xy-score XY-Scores,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	368 \| xy-weight XY-Weights
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	369 \| .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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	370 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	371
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	372 Ellipses (default = NA)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	373 \| 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.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	374 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	375
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	376 Sample colors (default = none)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	377 \| 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"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	378 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	379
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	380 Sample labels (default = none)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	381 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	382 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	383
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	384 Component to be displayed as abscissa (default = 1)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	385 \| In case of OPLS(-DA), the first component (i.e. the predictive component) must be set to 1"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	386 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	387
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	388 Component to be displayed as ordinate (default = 2)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	389 \| 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)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	390 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	391
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	392 Number of variables most contributing to loadings to be highlighted (default = 3)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	393 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	394 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	395
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	396 Advanced computational parameters
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	397 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	398
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	399 Scaling (default = standard)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	400 \| Either mean-centering alone (center), or followed by pareto scaling (pareto), or unit-variance scaling (standard)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	401 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	402
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	403 Permutation testing for (O)PLS(-DA) models: Number of permutations (default = 20)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	404 \| Number of random permutations of response labels to estimate R2Y and Q2Y significance; Default is 10 for single response models and 0 otherwise
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	405 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	406
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	407 Log10 transformation (default = no)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	408 \| Should the data matrix values be log10 transformed? Note: zeros are set to 1 prior to transformation
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	409 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	410
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	411 Train/test partition (default = none)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	412 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	413 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	414
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	415 Algorithm (default = svd for PCA and nipals for PLS and OPLS)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	416 \| 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	417 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	418
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	419 Number of cross-validation segments (default = 7)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	420 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	421
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	422
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	423 ------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	424 Output files
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	425 ------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	426
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	427
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	428 sampleMetadata_out.tabular
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	429 \| sampleMetadata tabular separated file identical to the file given as argument, except that two columns with the x-scores of the displayed components have been added
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	430 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	431
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	432 variableMetadata_out.tabular
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	433 \| variableMetadata tabular separated 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.
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	434 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	435
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	436 figure.pdf
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	437 \| Graphic
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	438 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	439
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	440 information.txt
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	441 \| Text file with all messages and warnings generated during the computation
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	442 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	443
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	444 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	445
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	446 ----------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	447 Working examples
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	448 ----------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	449
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	450 \|
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	451
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	452 .. class:: infomark
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	453
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	454 See the W4M00001a_sacurine-subset-statistics, W4M00001b_sacurine-complete, W4M00002_mtbls2 or W4M00003_diaplasma shared histories in the Shared Data/Published Histories menu (https://galaxy.workflow4metabolomics.org/history/list_published)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	455
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	456
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	457 Figure output
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	458 =============
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	459
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	460 .. image:: multivariate_workingExampleImage.png
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	461 :width: 600
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	462
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	463 ---------------------------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	464
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	465 ----
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	466 NEWS
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	467 ----
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	468
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	469 CHANGES IN VERSION 2.3.8
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	470 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	471
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	472 MINOR CORRECTION
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	473
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	474 (O)PLS(-DA) coefficients display in case of multiple quantitative (or multiclass) response: now the column names of the coefficients for each response are correctly labelled in the variableMetadata file
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	475
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	476 CHANGES IN VERSION 2.3.6
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	477 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	478
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	479 INTERNAL MODIFICATIONS
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	480
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	481 Minor internal modifications
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	482
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	483 CHANGES IN VERSION 2.3.4
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	484 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	485
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	486 INTERNAL MODIFICATIONS
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	487
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	488 Minor update in .shed.yml file
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	489
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	490 CHANGES IN VERSION 2.3.2
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	491 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	492
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	493 NEW FEATURES
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	494
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	495 Error messages are generated in OPLS(-DA) models in case of non-significance of either the predictive or the first orthogonal component
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	496
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	497 INTERNAL MODIFICATIONS
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	498
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	499 Modifications of the wrapper file to handle the recent ropls package versions (i.e. 1.3.15 and above) which use S4 classes
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	500
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	501 CHANGES IN VERSION 2.3.0
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	502 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	503
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	504 NEW FEATURES
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	505
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	506 1) Predictions now available (see the 'Samples to be tested' argument)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	507 2) OPLS(-DA): Predictive and Orthogonal VIP are now computed (see the 'comments' section)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	508 3) Multiclass PLS-DA implemented (see the 'comments' section)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	509
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	510 MINOR MODIFICATIONS
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	511
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	512 1) Changes in color palette: black/grey colors for diagnostics and other colors for scores
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	513 2) Default number of permutations set to 20 (instead of 10)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	514 3) Predictive components denoted in the tables by 'p' (instead of 'h' previously)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	515
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	516 CHANGES IN VERSION 2.2.4
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	517 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	518
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	519 1) Correction in the Galaxy wrapper (in the previous version, the number of predictive components was sometimes set to the maximum by mistake)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	520 2) The regression coefficients are now provided as a new column of the variableMetadata output
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	521
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	522 CHANGES IN VERSION 2.2.3
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	523 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	524
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	525 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	526
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	527 CHANGES IN VERSION 2.2.2
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	528 ========================
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	529
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	530 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
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	531 2) Classification is currently implemented for two-class responses only
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	532 3) dataMatrix is not modified by the tool, so it does not appear as an output files
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	533 4) Double cross-validation (advanced computational parameters): 'odd' now refers to train (instead to test) indices
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	534
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	535 </help>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	536
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	537 <citations>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	538 <citation type="bibtex">@Article{Thevenot2015,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	539 Title = {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},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	540 Author = {Thevenot, Etienne A. and Roux, Aurelie and Xu, Ying and Ezan, Eric and Junot, Christophe},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	541 Journal = {Journal of Proteome Research},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	542 Year = {2015},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	543 Note = {PMID: 26088811},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	544 Number = {8},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	545 Pages = {3322-3335},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	546 Volume = {14},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	547
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	548 Doi = {10.1021/acs.jproteome.5b00354},
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	549 Url = {http://pubs.acs.org/doi/full/10.1021/acs.jproteome.5b00354}
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	550 }</citation>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	551 <citation type="doi">10.1093/bioinformatics/btu813</citation>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	552 </citations>
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	553
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4 ethevenot parents: diff changeset	554 </tool>

Mercurial > repos > ethevenot > multivariate

annotate multivariate_config.xml @ 1:60c360e466a8 draft default tip