Mercurial > repos > ethevenot > checkformat
annotate README.md @ 0:059eb452931e draft
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author | ethevenot |
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date | Tue, 24 Oct 2017 08:44:02 -0400 |
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children | b642f4f87022 |
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059eb452931e
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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1 Checking the formats of the dataMatrix, sampleMetadata, and variableMetadata files |
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2 ================================================================================== |
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3 |
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4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure |
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5 |
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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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7 |
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8 ### Description |
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9 |
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10 **Version:** 2.0.4 |
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11 **Date:** 2016-07-29 |
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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) |
059eb452931e
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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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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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
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20 |
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21 ### Installation |
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22 |
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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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28 |
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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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32 |
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33 ### Tests |
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34 |
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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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36 |
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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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41 |
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42 ### Working example |
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43 |
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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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45 |
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46 ### News |
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47 |
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48 ##### CHANGES IN VERSION 2.0.4 |
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49 |
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50 INTERNAL MODIFICATION |
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51 |
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52 * Minor internal modifications |
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53 |
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54 ##### CHANGES IN VERSION 2.0.2 |
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55 |
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56 INTERNAL MODIFICATION |
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57 |
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58 * Creating tests for R code |