diff README.md @ 2:09799fc16bc6 draft

planemo upload for repository https://github.com/workflow4metabolomics/univariate.git commit 2c0d4d97c208edca1ada2035a7b7af9c4eb31afe

--- a/README.md	Sat Jul 30 12:38:02 2016 -0400
+++ b/README.md	Sat Aug 06 12:42:42 2016 -0400
@@ -1,13 +1,14 @@
-# Univariate parametric and non-parametric hypothesis testing with correction for multiple testing
+Univariate parametric and non-parametric hypothesis testing with correction for multiple testing  
+================================================================================================  
 
-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/univariate.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/univariate).
 
-## Description
+### Description
 
-**Version:** 2.1.2   
-**Date:** 2016-07-30  
+**Version:** 2.1.4   
+**Date:** 2016-08-05  
 **Author:** Marie Tremblay-Franco (INRA, MetaToul, MetaboHUB, W4M Core Development Team) and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)    
 **Email:** [marie.tremblay-franco(at)toulouse.inra.fr](mailto:[e-mail]); [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)  
@@ -15,27 +16,58 @@
 **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
+### Installation
 
- * Configuration file: **univariate_config.xml**  
+ * Configuration file: `univariate_config.xml`  
  * Image file: 
-  + **static/images/univariate_workflowPositionImage.png**   
- * Wrapper file: **univariate_wrapper.R**  
- * Script file: **univariate_script.R**  
+  + `static/images/univariate_workflowPositionImage.png`   
+ * Wrapper file: `univariate_wrapper.R`  
+ * Script file: `univariate_script.R`  
  * R packages  
-  + **batch** from CRAN: `install.packages("batch", dep=TRUE)`.
-  + **PMCMR** from Bioconductor: `install.packages("PMCMR", dep=TRUE)`.
+  + **batch** from CRAN  
+  
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+  + **PMCMR** from CRAN  
+  
+    ```r  
+    install.packages("PMCMR", dep=TRUE)  
+    ```    
+ 
+### Tests
 
-## Tests
+The code in the wrapper can be tested by running the `runit/univariate_runtests.R` R file
+
+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/univariate_tests.R** in R  
+### 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 2.1.4
+
+NEW FEATURE  
 
-## News
+Level names are now separated by '.' instead of '-' previously in the column names of the output variableMetadata table (e.g., 'jour_ttest_J3.J10_fdr' instead of 'jour_ttest_J3-J10_fdr' previously)  
+
+INTERNAL MODIFICATION  
 
-## CHANGES IN VERSION 2.1.2  
+ * Minor internal changes  
+
+###### CHANGES IN VERSION 2.1.2  
+
+INTERNAL MODIFICATION  
 
  * Minor internal changes in .shed.yml for toolshed export
 
-## CHANGES IN VERSION 2.1.1  
+###### CHANGES IN VERSION 2.1.1  
+
+INTERNAL MODIFICATION  
 
  * Internal handling of 'NA' p-values (e.g. when intensities are identical in all samples).