Mercurial > repos > ethevenot > transformation
annotate README.md @ 1:d9e05021553c draft
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
author | ethevenot |
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date | Sat, 06 Aug 2016 12:02:52 -0400 |
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d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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1 Transformation of the data matrix |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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2 ================================= |
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3 |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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5 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/transformation.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/transformation). |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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7 |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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8 ### Description |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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9 |
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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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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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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) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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15 **Licence:** CeCILL |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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16 **Reference history:** [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published) |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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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) |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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18 |
eacea1349a7c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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19 ### Installation |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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20 |
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21 * Configuration file: `transformation_config.xml` |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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22 * Image files: `static/images/transformation_workflowPositionImage.png` |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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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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26 |
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27 ```r |
d9e05021553c
planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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28 install.packages("batch", dep=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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29 ``` |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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30 |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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31 ### Tests |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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32 |
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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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34 |
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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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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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38 ``` |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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39 |
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40 ### Working example |
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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit c4b65942d74d5bdfd46e748c0040a8b5ebe4fd1d
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41 |
d9e05021553c
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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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planemo upload for repository https://github.com/workflow4metabolomics/transformation.git commit 83f2d1045c0bf086bbe2de5204cd5c1d8354116f
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43 |
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44 ### News |
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45 |
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46 ##### CHANGES IN VERSION 2.2.0 |
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47 |
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48 NEW FEATURE |
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49 |
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50 * Square root transformation now available |
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51 |
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52 ##### CHANGES IN VERSION 2.0.2 |
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53 |
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54 INTERNAL MODIFICATION |
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55 |
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56 * Creating tests for R code |