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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab
author ethevenot
date Tue, 06 Jun 2017 11:44:00 -0400
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1 Discovery of significant signatures from omics data
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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/biosigner.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/biosigner).
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8 ### Description
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10 **Version:** 2.2.6
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11 **Date:** 2016-08-05
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12 **Author:** Philippe Rinaudo 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:** Rinaudo P., Boudah S., Junot C. and Thevenot E.A. (2015). biosigner: A new method for the discovery of restricted and stable molecular signatures from omics data. *Frontiers in Molecular Biosciences*, in review.
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15 **Licence:** CeCILL
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16 **Reference history:** [W4M00003_diaplasma](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: `biosigner_config.xml`
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22 * Image files:
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23 + `static/images/biosigner_workflowPositionImage.png`
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24 + `static/images/biosigner_workingExampleImage.png`
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25 * Wrapper file: `biosigner_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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32 + **biosigner** from Bioconductor
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34 ```r
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35 source("http://www.bioconductor.org/biocLite.R")
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36 biocLite("biosigner")
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37 ```
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39 ### Tests
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41 The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file
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43 You will need to install **RUnit** package in order to make it run:
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44 ```r
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45 install.packages('RUnit', dependencies = TRUE)
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46 ```
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48 ### Working example
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50 See the **W4M00001a_sacurine-subset-statistics** or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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52 ### News
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54 ###### CHANGES IN VERSION 2.2.6
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56 INTERNAL MODIFICATION
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58 * Minor internal modifications
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60 ###### CHANGES IN VERSION 2.2.4
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62 INTERNAL MODIFICATION
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64 * Internal updates for planemo and travis validation
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66 ###### CHANGES IN VERSION 2.2.2
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68 INTERNAL MODIFICATION
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70 * Internal updates to biosigner package versions of 1.0.0 and above, and ropls versions of 1.4.0 and above (i.e. using S4 methods instead of S3)
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72 ###### CHANGES IN VERSION 2.2.1
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74 NEW FEATURE
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76 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)