diff README.md @ 2:fa173e12e185 draft

planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 9f4dfcdc64aa9ac2a2f6d613cc33961c02fec254-dirty

--- a/README.md	Sat Jul 30 12:31:20 2016 -0400
+++ b/README.md	Sat Aug 06 12:07:13 2016 -0400
@@ -1,14 +1,14 @@
 Multivariate analysis by PCA, PLS(-DA), and OPLS(-DA)
 =====================================================
 
-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/multivariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/multivariate).
 
-## Description
+### Description
 
-**Version:** 2.3.4  
-**Date:** 2016-07-30  
+**Version:** 2.3.6  
+**Date:** 2016-08-05  
 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)   
 **Email:** [etienne.thevenot(at)cea.fr](mailto:[e-mail])  
 **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)  
@@ -16,13 +16,13 @@
 **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)
 
-## Installation
+### Installation
 
-* Configuration file: `multivariate_config.xml`.
+* Configuration file: `multivariate_config.xml` 
 * Image files: 
-  + `static/images/multivariate_workflowPositionImage.png`.
-  + `static/images/multivariate_workingExampleImage.png`.
-* Wrapper file: `multivariate_wrapper.R`.
+  + `static/images/multivariate_workflowPositionImage.png` 
+  + `static/images/multivariate_workingExampleImage.png` 
+* Wrapper file: `multivariate_wrapper.R` 
 * R packages  
   + **batch** from CRAN  
   
@@ -37,39 +37,43 @@
     biocLite("ropls")      
     ```
 
-## Tests
+### Tests
 
-The code in the wrapper can be tested by running the `tests/multivariate_tests.R` in R.
+The code in the wrapper can be tested by running the `runit/multivariate_runtests.R` R file
 
 You will need to install **RUnit** package in order to make it run:
 ```r
 install.packages('RUnit', dependencies = TRUE)
 ```
 
-## News
+### Working example  
+
+See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-subset-complete**, **W4M00002_mtbls2**, **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) 
+
+### News
 
-### CHANGES IN VERSION 2.3.4
+###### CHANGES IN VERSION 2.3.6  
+
+INTERNAL MODIFICATION  
+
+ * minor internal modifications  
+
+###### CHANGES IN VERSION 2.3.4
 
 INTERNAL MODIFICATION  
 
  * minor update of .shed.yml
-    
-***
 
-### CHANGES IN VERSION 2.3.2
+###### 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).
-    
-***
+ * 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
+###### 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).
-
-***
+ * **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)