diff README.md @ 0:fafba524dca6 draft

planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
author ethevenot
date Wed, 27 Jul 2016 11:22:56 -0400
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+Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)
+=====================================================
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project
+
+Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate).
+
+## Description
+
+**Version:** 2.3.2  
+**Date:** 2016-05-15  
+**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  
+**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)
+
+## Installation
+
+* Configuration file: `multivariate_config.xml`.
+* Image files: 
+  + `static/images/multivariate_workflowPositionImage.png`.
+  + `static/images/multivariate_workingExampleImage.png`.
+* Wrapper file: `multivariate_wrapper.R`.
+* R packages  
+  + **batch** from CRAN  
+  
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+
+  + **ropls** from Bioconductor  
+  
+    ```r
+    install.packages("batch", dep=TRUE)  
+    source("http://www.bioconductor.org/biocLite.R")  
+    biocLite("ropls")      
+    ```
+
+## Tests
+
+The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R.
+
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
+
+## News
+
+### CHANGES IN VERSION 2.3.2
+
+INTERNAL MODIFICATION  
+
+ * Modification of the `multivariate_wrapper.R` file to handle **ropls** package versions of 1.3.15 and above (i.e. after switching to S4 classes).
+    
+***
+
+### CHANGES IN VERSION 2.3.0
+
+NEW FEATURES  
+
+ * **Predictions** now available (see the 'Samples to be tested' argument).
+ * OPLS(-DA): **Predictive and Orthogonal VIP** are now computed (see the 'comments' section).
+ * **Multiclass PLS-DA** implemented (see the 'comments' section).
+
+***