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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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comparison
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1 Metrics and graphics to assess the quality of the data
2 ======================================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/qualitymetrics.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/qualitymetrics).
7
8 ### Description
9
10 **Version:** 2.2.4
11 **Date:** 2016-08-04
12 **Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)
13 **Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
14 **Citation:**
15 **Licence:** CeCILL
16 **Reference history:** [W4M00001b_sacurine-complete](http://galaxy.workflow4metabolomics.org/history/list_published)
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)
18
19 ### Installation
20
21 * Configuration file:
22 + `qualitymetrics_config.xml`
23 * Image files:
24 + `static/images/QualityControl.png`
25 + `static/images/qualitymetrics_workingExampleImage.png`
26 * Wrapper file:
27 + `qualitymetrics_wrapper.R`
28 * Script file:
29 + `qualitymetrics_script.R`
30 * R packages
31 + **batch** from CRAN
32
33 ```r
34 install.packages("batch", dep=TRUE)
35 ```
36
37 + **ropls** from Bioconductor
38
39 ```r
40 source("http://www.bioconductor.org/biocLite.R")
41 biocLite("ropls")
42 ```
43
44 ### Tests
45
46 The code in the wrapper can be tested by running the `runit/qualitymetrics_runtests.R` R file
47
48 You will need to install **RUnit** package in order to make it run:
49 ```r
50 install.packages('RUnit', dependencies = TRUE)
51 ```
52
53 ### News
54
55 ##### CHANGES IN VERSION 2.2.4
56
57 INTERNAL MODIFICATION
58
59 * Additional running and installation tests added with planemo, conda, and travis
60
61 ##### CHANGES IN VERSION 2.2.3
62
63 INTERNAL MODIFICATION
64
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
66
67 * Creating tests for the R code
68
69 ##### CHANGES IN VERSION 2.2.2
70
71 INTERNAL MODIFICATION
72
73 * Minor internal modification