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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 60ebb3e8919c09c18f89a5362750ae45ca84d0c2
author ethevenot
date Wed, 28 Feb 2018 09:15:47 -0500
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1 Transformation of the data matrix
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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/transformation.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/transformation).
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8 ### Description
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10 **Version:** 2.2.0
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11 **Date:** 2016-08-04
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12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
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13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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14 **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)
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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: `transformation_config.xml`
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22 * Image files: `static/images/transformation_workflowPositionImage.png`
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23 * Wrapper file: `transformation_wrapper.R`
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24 * R packages
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25 + **batch** from CRAN
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27 ```r
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28 install.packages("batch", dep=TRUE)
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29 ```
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31 ### Tests
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33 The code in the wrapper can be tested by running the `runit/transformation_runtests.R` R file
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35 You will need to install **RUnit** package in order to make it run:
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36 ```r
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37 install.packages('RUnit', dependencies = TRUE)
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38 ```
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40 ### Working example
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42 See the **W4M00001b_sacurine-complete** or **W4M00002_mtbls2** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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44 ### News
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46 ##### CHANGES IN VERSION 2.2.0
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48 NEW FEATURE
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50 * Square root transformation now available
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52 ##### CHANGES IN VERSION 2.0.2
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54 INTERNAL MODIFICATION
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56 * Creating tests for R code