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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 6b7aa0db6cebdb8acfac0a07291647947260a310
author ethevenot
date Thu, 01 Mar 2018 05:09:49 -0500
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1 Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files
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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/checkformat.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/checkformat).
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8 ### Description
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10 **Version:** 3.0.0
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11 **Date:** 2018-01-10
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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 histories:**
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17 [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published),
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18 [W4M00002_sacurine_mtbls2](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00003_sacurine_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published)
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19 **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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21 ### Installation
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23 * Configuration file: `checkformat_config.xml`
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24 * Image file: `static/images/checkformat_workflowPositionImage.png`
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25 * Wrapper file: `checkformat_wrapper.R`
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26 * R packages
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27 + **batch** from CRAN
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29 ```r
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30 install.packages("batch", dep=TRUE)
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31 ```
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33 ### Tests
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35 The code in the wrapper can be tested by running the `runit/checkformat_tests.R` R file
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37 You will need to install **RUnit** package in order to make it run:
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38 ```r
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39 install.packages('RUnit', dependencies = TRUE)
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40 ```
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42 ### Working example
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44 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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46 ### News
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48 ##### CHANGES IN VERSION 3.0.0
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50 NEW FEATURES
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52 * Automated re-ordering (if necessary) of sample and/or variable names from dataMatrix based on sampleMetadata and variableMetadata
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54 * New argument to make sample and variable names syntactically valid
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56 * Output of dataMatrix, sampleMetadata, and variableMetadata files, whether they have been modified or not
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58 ##### CHANGES IN VERSION 2.0.4
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60 INTERNAL MODIFICATION
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62 * Minor internal modifications
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64 ##### CHANGES IN VERSION 2.0.2
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66 INTERNAL MODIFICATION
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68 * Creating tests for R code