diff README.md @ 2:b2414be87d4b draft

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

--- a/README.md	Sat Jul 30 12:21:07 2016 -0400
+++ b/README.md	Sat Aug 06 12:17:12 2016 -0400
@@ -1,14 +1,14 @@
 Discovery of significant signatures from omics data
 ===================================================
 
-A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project
+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
+### Description
 
-**Version:** 2.2.4  
-**Date:** 2016-07-30   
+**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.   
@@ -16,31 +16,61 @@
 **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
+### Installation
 
-* Configuration file: `biosigner_config.xml`.
+* 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: `install.packages("batch", dep=TRUE)`.
-  + **biosigner** from Bioconductor (which itself depends on **ropls** from Bioconductor and **e1071** and **randomForest** from CRAN): `source("http://www.bioconductor.org/biocLite.R") ; biocLite("biosigner")`.
+  + `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
 
-## Tests
+You will need to install **RUnit** package in order to make it run:
+```r
+install.packages('RUnit', dependencies = TRUE)
+```
 
-The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R  
+### 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
+### News
+
+###### CHANGES IN VERSION 2.2.6  
 
-## CHANGES IN VERSION 2.2.4
+INTERNAL MODIFICATION  
+
+ * Minor internal modifications
+ 
+###### CHANGES IN VERSION 2.2.4  
 
- * Internal updates for planemo and travis validation
+INTERNAL MODIFICATION  
+
+ * Internal updates for planemo and travis validation  
  
-## CHANGES IN VERSION 2.2.2
+###### 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
+###### 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)