Mercurial > repos > ethevenot > biosigner
diff README.md @ 2:b2414be87d4b draft
planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
author | ethevenot |
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date | Sat, 06 Aug 2016 12:17:12 -0400 |
parents | 4ff502a46189 |
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--- a/README.md Sat Jul 30 12:21:07 2016 -0400 +++ b/README.md Sat Aug 06 12:17:12 2016 -0400 @@ -1,14 +1,14 @@ Discovery of significant signatures from omics data =================================================== -A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure Status: [](https://travis-ci.org/workflow4metabolomics/biosigner). -## Description +### Description -**Version:** 2.2.4 -**Date:** 2016-07-30 +**Version:** 2.2.6 +**Date:** 2016-08-05 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **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. @@ -16,31 +16,61 @@ **Reference history:** [W4M00003_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published) **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) -## Installation +### Installation -* Configuration file: `biosigner_config.xml`. +* Configuration file: `biosigner_config.xml` * Image files: - + `static/images/biosigner_workflowPositionImage.png`. - + `static/images/biosigner_workingExampleImage.png`. -* Wrapper file: `biosigner_wrapper.R`. -* R packages - + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. - + **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")`. + + `static/images/biosigner_workflowPositionImage.png` + + `static/images/biosigner_workingExampleImage.png` +* Wrapper file: `biosigner_wrapper.R` +* R packages + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + ``` + + **biosigner** from Bioconductor + + ```r + source("http://www.bioconductor.org/biocLite.R") + biocLite("biosigner") + ``` + +### Tests + +The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file -## Tests +You will need to install **RUnit** package in order to make it run: +```r +install.packages('RUnit', dependencies = TRUE) +``` -The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R +### Working example + +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) -## News +### News + +###### CHANGES IN VERSION 2.2.6 -## CHANGES IN VERSION 2.2.4 +INTERNAL MODIFICATION + + * Minor internal modifications + +###### CHANGES IN VERSION 2.2.4 - * Internal updates for planemo and travis validation +INTERNAL MODIFICATION + + * Internal updates for planemo and travis validation -## CHANGES IN VERSION 2.2.2 +###### CHANGES IN VERSION 2.2.2 + +INTERNAL MODIFICATION * 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) -## CHANGES IN VERSION 2.2.1 +###### CHANGES IN VERSION 2.2.1 + +NEW FEATURE * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)