annotate README.md @ 0:48e4be935243 draft

planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
author ethevenot
date Wed, 27 Jul 2016 11:40:20 -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) project
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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:** 2.2.2
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11 **Date:** 2016-05-21
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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: `install.packages("batch", dep=TRUE)`.
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28 + **biosigner** from Bioconductor (which itself depends on **ropls** from Bioconductor and **e1071** and **randomForest** from CRAN): `source("http://www.bioconductor.org/biocLite.R") ; biocLite("biosigner")`.
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30 ## Tests
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32 The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R
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34 ## News
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36 ## CHANGES IN VERSION 2.2.2
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38 * 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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40 ## CHANGES IN VERSION 2.2.1
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42 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)