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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
author ethevenot
date Sat, 06 Aug 2016 12:01:17 -0400
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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1 Metrics and graphics to assess the quality of the data
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2 ======================================================
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/qualitymetrics.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/qualitymetrics).
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8 ### Description
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10 **Version:** 2.2.4
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11 **Date:** 2016-08-04
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12 **Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
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13 **Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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14 **Citation:**
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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17 **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)
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19 ### Installation
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21 * Configuration file:
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22 + `qualitymetrics_config.xml`
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23 * Image files:
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24 + `static/images/QualityControl.png`
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25 + `static/images/qualitymetrics_workingExampleImage.png`
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26 * Wrapper file:
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27 + `qualitymetrics_wrapper.R`
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28 * Script file:
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29 + `qualitymetrics_script.R`
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30 * R packages
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31 + **batch** from CRAN
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33 ```r
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34 install.packages("batch", dep=TRUE)
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35 ```
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37 + **ropls** from Bioconductor
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39 ```r
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40 source("http://www.bioconductor.org/biocLite.R")
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41 biocLite("ropls")
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42 ```
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44 ### Tests
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46 The code in the wrapper can be tested by running the `runit/qualitymetrics_runtests.R` R file
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48 You will need to install **RUnit** package in order to make it run:
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49 ```r
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50 install.packages('RUnit', dependencies = TRUE)
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51 ```
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53 ### News
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55 ##### CHANGES IN VERSION 2.2.4
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57 INTERNAL MODIFICATION
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59 * Additional running and installation tests added with planemo, conda, and travis
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61 ##### CHANGES IN VERSION 2.2.3
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63 INTERNAL MODIFICATION
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65 * 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
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67 * Creating tests for the R code
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69 ##### CHANGES IN VERSION 2.2.2
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71 INTERNAL MODIFICATION
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73 * Minor internal modification