Mercurial > repos > ethevenot > multivariate
changeset 3:e91de3b04320 draft
planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit bb92582ec396fd845b49454c4cadd86fbfc73fab
| author | ethevenot |
|---|---|
| date | Sat, 22 Oct 2016 03:02:47 -0400 |
| parents | fa173e12e185 |
| children | 5526f8258e8a |
| files | README.md build.xml multivariate_config.xml multivariate_wrapper.R |
| diffstat | 4 files changed, 24 insertions(+), 8 deletions(-) [+] |
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--- a/README.md Sat Aug 06 12:07:13 2016 -0400 +++ b/README.md Sat Oct 22 03:02:47 2016 -0400 @@ -7,12 +7,12 @@ ### Description -**Version:** 2.3.6 -**Date:** 2016-08-05 +**Version:** 2.3.8 +**Date:** 2016-10-21 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** 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. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) -**Licence:** CeCILL +**Licence:** CeCILL **Reference history:** [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) @@ -52,6 +52,12 @@ ### News +###### CHANGES IN VERSION 2.3.8 + +MINOR MODIFICATION + + * (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 + ###### CHANGES IN VERSION 2.3.6 INTERNAL MODIFICATION
--- a/build.xml Sat Aug 06 12:07:13 2016 -0400 +++ b/build.xml Sat Oct 22 03:02:47 2016 -0400 @@ -36,7 +36,7 @@ <arg value="--conda_prefix"/> <arg value="${conda.dir}"/> <arg value="--galaxy_branch"/> - <arg value="release_16.01"/> + <arg value="release_16.07"/> <arg value="--conda_dependency_resolution"/> <arg value="${tool.xml}"/> </exec>
--- a/multivariate_config.xml Sat Aug 06 12:07:13 2016 -0400 +++ b/multivariate_config.xml Sat Oct 22 03:02:47 2016 -0400 @@ -1,10 +1,10 @@ -<tool id="Multivariate" name="Multivariate" version="2.3.6"> +<tool id="Multivariate" name="Multivariate" version="2.3.8"> <description>PCA, PLS and OPLS</description> <requirements> - <requirement type="package" version="3.2.2">R</requirement> + <requirement type="package" version="3.3.1">R</requirement> <requirement type="package">r-batch</requirement> - <requirement type="package" version="1.4.2">bioconductor-ropls</requirement> + <requirement type="package">bioconductor-ropls</requirement> </requirements> <stdio> @@ -458,6 +458,13 @@ NEWS ---- +CHANGES IN VERSION 2.3.8 +======================== + +MINOR CORRECTION + +(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 + CHANGES IN VERSION 2.3.6 ========================
--- a/multivariate_wrapper.R Sat Aug 06 12:07:13 2016 -0400 +++ b/multivariate_wrapper.R Sat Oct 22 03:02:47 2016 -0400 @@ -398,7 +398,10 @@ } if(!is.null(coeMN)) { pCompMN <- cbind(pCompMN, coeMN) - colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC, "_COEFF") + if(ncol(coeMN) == 1) + colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC, "_COEFF") + else + colnames(pCompMN)[(ncol(pCompMN) - ncol(coeMN) + 1):ncol(pCompMN)] <- paste0(rspModC, "_", colnames(coeMN), "-COEFF") } pCompDF <- as.data.frame(pCompMN)[rownames(varDF), , drop = FALSE] varDF <- cbind.data.frame(varDF, pCompDF)