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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit d7c2aaa255108244f5be6fb7e48b3dec76422ebe
author ethevenot
date Wed, 28 Feb 2018 11:29:46 -0500
parents 5215be2bdc9e
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1 Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS)
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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/profia.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/profia).
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8 ### Description
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10 **Version:** 3.1.0
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11 **Date:** 2018-01-08
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12 **Author:** Alexis Delabriere and 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:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. (2017). proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, 33:3767-3775 (https://doi.org/10.1093/bioinformatics/btx458).
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15 **Licence:** CeCILL
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16 **Reference history:**
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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: `profia_config.xml`
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22 * Image files:
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23 + `static/images/profia_workflowPositionImage.png`
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24 + `static/images/profia_workingExampleImage.png`
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25 * Wrapper file: `profia_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 install.packages("minpack.lm", dep=TRUE)
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32 install.packages("missForest", dep=TRUE)
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33 install.packages("pracma", dep=TRUE)
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34 ```
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35 + **profia** from Bioconductor
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37 ```r
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38 source("http://www.bioconductor.org/biocLite.R")
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39 biocLite("Biobase")
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40 biocLite("BiocParallel")
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41 biocLite("xcms")
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42 biocLite("plasFIA")
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43 biocLite("proFIA")
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44 ```
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46 ### Tests
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48 The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file
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50 You will need to install **RUnit** package in order to make it run:
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51 ```r
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52 install.packages('RUnit', dependencies = TRUE)
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53 ```
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55 ### Working example
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57 ### News
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59 ###### CHANGES IN VERSION 3.1.0
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61 NEW FEATURE
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63 randomForest method implemented for imputation of missing values
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65 ###### CHANGES IN VERSION 3.0.6
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67 NEW FEATURES
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69 * New (advanced) parameters available
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71 ###### CHANGES IN VERSION 3.0.4
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73 MINOR MODIFICATION
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75 * Details added in the documentation
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77 ###### CHANGES IN VERSION 3.0.2
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79 NEW FEATURE
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81 * Parallel processing
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83 ###### CHANGES IN VERSION 3.0.0
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85 NEW FEATURE
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87 * Creation of the tool