annotate README.md @ 2:b2414be87d4b draft

planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79

Discovery of significant signatures from omics data
===================================================

A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure  

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

### Description

**Version:** 2.2.6  
**Date:** 2016-08-05     
**Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)   
**Email:** [etienne.thevenot(at)cea.fr](mailto:[e-mail])  
**Citation:** Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. *Frontiers in Molecular Biosciences*, in review.   
**Licence:** CeCILL
**Reference history:** [W4M00003_diaplasma](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 file: `biosigner_config.xml`
* Image files: 
  + `static/images/biosigner_workflowPositionImage.png`   
  + `static/images/biosigner_workingExampleImage.png`
* Wrapper file: `biosigner_wrapper.R`
* R packages
 + **batch** from CRAN  
  
    ```r
    install.packages("batch", dep=TRUE)  
    ```
  + **biosigner** from Bioconductor  
  
    ```r
    source("http://www.bioconductor.org/biocLite.R")  
    biocLite("biosigner")
    ```  

### Tests

The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file

You will need to install **RUnit** package in order to make it run:
```r
install.packages('RUnit', dependencies = TRUE)
```

### Working example  

See the **W4M00001a_sacurine-subset-statistics** or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)  

### News

###### CHANGES IN VERSION 2.2.6  

INTERNAL MODIFICATION  

 * Minor internal modifications
 
###### CHANGES IN VERSION 2.2.4  

INTERNAL MODIFICATION  

 * Internal updates for planemo and travis validation  
 
###### CHANGES IN VERSION 2.2.2  

INTERNAL MODIFICATION  

 * Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)
    
###### CHANGES IN VERSION 2.2.1

NEW FEATURE

 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)