Mercurial > repos > ethevenot > qualitymetrics

Metrics and graphics to assess the quality of the data
======================================================

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

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

### Description

**Version:** 2.2.4
**Date:** 2016-08-04
**Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
**Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
**Citation:**
**Licence:** CeCILL
**Reference history:** [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

* Configuration file:
    + `qualitymetrics_config.xml`
* Image files:
    + `static/images/QualityControl.png`
    + `static/images/qualitymetrics_workingExampleImage.png`
* Wrapper file:
    + `qualitymetrics_wrapper.R`
* Script file:
    + `qualitymetrics_script.R`
* R packages
  + **batch** from CRAN

    ```r
    install.packages("batch", dep=TRUE)
    ```

  + **ropls** from Bioconductor

    ```r
    source("http://www.bioconductor.org/biocLite.R")
    biocLite("ropls")
    ```

### Tests

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

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

### News

##### CHANGES IN VERSION 2.2.4

INTERNAL MODIFICATION

 * Additional running and installation tests added with planemo, conda, and travis

##### CHANGES IN VERSION 2.2.3

INTERNAL MODIFICATION

 * Modifications of the 'qualitymetrics_script.R' file to handle the recent 'ropls' package versions (i.e. 1.3.15 and above) which use S4 classes

 * Creating tests for the R code

##### CHANGES IN VERSION 2.2.2

INTERNAL MODIFICATION

 * Minor internal modification
author	ethevenot
date	Sat, 06 Aug 2016 12:01:17 -0400
parents
children	6d3b7b6573d8