comparison README.md @ 0:b74d1d533dea draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde

0:b74d1d533dea

## Signal drift and batch-effect correction  
#### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project

Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batchcorrection.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batchcorrection).

### Description

**Version:** 2.0.6  
**Date:** 2016-08-02  
**Author:** Jean-François Martin (INRA, AXIOM), Mélanie Pétéra (INRA, PFEM), Marion Landi (INRA, PFEM), Franck Giacomoni (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)  
**Email:** [jean-francois.martin(at)toulouse.inra.fr](mailto:[e-mail]), [melanie.petera(at)clermont.inra.fr](mailto:[e-mail]), [etienne.thevenot(at)cea.fr](mailto:[e-mail])  
**Citation:**  
**Licence:** CeCILL  
**Reference history:** [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)  

### Installation

* Configuration files:
    + **batch_correction.xml** (for the "Batch Correction" module)
    + **determine_bc.xml** (for the "Determine Batch Correction" module)  
* Image files: 
    + **static/images/batch_correction.png**    
    + **static/images/determine_batch_correction.png**  
    + **static/images/pdf_plotsituation.png**    
    + **static/images/Vdk_pdf1.png**    
    + **static/images/Vdk_pdf2.png**        
* Wrapper files:
    + **batch_correction_wrapper.R**  
    + **batch_correction_all_loess_wrapper.R**  
* Script files:
    + **Normalisation_QCpool.r**  
    + **miniTools.R**  
    + **RcheckLibrary.R**  
    + **batch_correction_all_loess_script.R**  
* R packages  
    + **batch** from CRAN      
> install.packages("batch", dep=TRUE)  
    + **ade4** from CRAN      
> install.packages("ade4", dep=TRUE)
    + **pcaMethods** from Bioconductor  
> source("http://www.bioconductor.org/biocLite.R")  
> biocLite("pcaMethods")          
    + **ropls** from Bioconductor  
> source("http://www.bioconductor.org/biocLite.R")  
> biocLite("ropls")      

### Tests

The code in the batch_correction_wrapper can be tested by running the **runit/batchcorrection_runtests.R** in R  

### News

##### CHANGES IN VERSION 2.0.6

INTERNAL MODIFICATIONS

    o Additional running and installation tests added with planemo, conda, and travis

##### CHANGES IN VERSION 2.0.4

INTERNAL MODIFICATION  

    o Modification of the 'all_loess_wrapper.R' file to handle 'ropls' package versions of 1.3.15 and above (i.e. after switching to S4 classes)
    
***