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+Signal drift and batch-effect correction  
+========================================
+
+A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure  
+
+Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/batch_correction.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/batch_correction).
+
+### Description
+
+**Version:** 3.0.0  
+**Date:** 2020-10-02    
+**Author:** Jean-Francois Martin (INRAE, AXIOM), Melanie Petera (INRAE, PFEM), Marion Landi (PFEM), Franck Giacomoni (INRAE, PFEM), and Etienne A. Thevenot (CEA, LIST)  
+**Email:** [jean-francois.martin(at)inrae.fr](mailto:[e-mail]), [melanie.petera(at)inrae.fr](mailto:[e-mail]), [etienne.thevenot(at)cea.fr](mailto:[e-mail])  
+**Citation:**  
+**Licence:** CeCILL  
+**Reference history:** [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12)  
+**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`          
+* Wrapper files:
+    + `batch_correction_3Lwrapper.R`  
+    + `batch_correction_all_loess_wrapper.R`  
+* Script files:
+    + `batch_correction_3Lfct.R`  
+    + `batch_correction_3Llauncher.R`
+    + `batch_correction_all_loess_script.R`  
+* R packages
+  + **batch** from CRAN  
+  
+    ```r
+    install.packages("batch", dep=TRUE)  
+    ```
+
+  + **ade4** from CRAN  
+  
+    ```r
+    install.packages("ade4", dep=TRUE)  
+    ```
+
+ + **pcaMethods** from Bioconductor  
+  
+    ```r
+    source("http://www.bioconductor.org/biocLite.R")  
+    biocLite("pcaMethods")      
+    ```
+
+ + **ropls** from Bioconductor  
+  
+    ```r
+    source("http://www.bioconductor.org/biocLite.R")  
+    biocLite("ropls")      
+    ```
+
+### Tests
+
+Some functional tests are provided in Galaxy format (see XML wrapper and test-data folder).
+
+WIP: The code in the batch_correction_wrapper can be tested by running the `test/batchcorrection_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 reference histories [W4M00001_Sacurine-statistics; DOI:10.15454/1.4811121736910142E12](http://dx.doi.org/10.15454/1.4811121736910142E12) and [W4M00002_Sacurine-comprehensive; DOI:10.15454/1.481114233733302E12](http://dx.doi.org/10.15454/1.481114233733302E12)  
+ 
+
+### News
+
+###### CHANGES IN VERSION 3.0.0  
+
+NEW FEATURES 
+
+ * Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata are now available in a dedicated parameter section
+ * Addition of a sum of ions before/after plot for linear/lowess/loess methods
+ * Addition of a third option in "Null values" parameter (renamed "unconsistant values") in linear/lowess/loess methods
+ * linear/lowess/loess methods now handle NA in intensities and allow "blank" samples in the dataset
+
+INTERNAL MODIFICATIONS
+
+ * XML optimisation using macros
+ * Output name changes
+ * linear/lowess/loess methods: disabling of RData output
+ * linear/lowess/loess methods: split of tool-linked code and script-linked one
+ * linear/lowess/loess methods: adjustments in the normalisation process to match matters linked to NA acceptance
+ * linear/lowess/loess methods: better handling of special characters in IDs and column names
+
+###### CHANGES IN VERSION 2.2.4  
+
+INTERNAL MODIFICATIONS  
+
+Fixed bug for pool selection ("all_loess" methods)
+
+###### CHANGES IN VERSION 2.2.2  
+
+INTERNAL MODIFICATIONS  
+
+Fixed bug for color plot ("all_loess" methods)  
+
+###### CHANGES IN VERSION 2.2.0  
+
+NEW FEATURE  
+
+Specific names for the 'sampleType', 'injectionOrder', and 'batch' from sampleMetadata can be selected by the user (for compatibility with the MTBLS downloader)  
+
+##### CHANGES IN VERSION 2.1.2  
+
+INTERNAL MODIFICATIONS  
+
+ * Minor modifications in config file  
+
+##### CHANGES IN VERSION 2.1.0  
+
+INTERNAL MODIFICATIONS  
+
+ * For PCA figure display only ("all_loess_" options): missing values are set to the minimum value before PCA computation is performed (with svd)
+ 
+ * Additional running and installation tests added with planemo, conda, and travis  
+
+ * 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)