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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
author ethevenot
date Sat, 06 Aug 2016 12:17:12 -0400
parents 4ff502a46189
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1 Discovery of significant signatures from omics data 1 Discovery of significant signatures from omics data
2 =================================================== 2 ===================================================
3 3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project 4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
5 5
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/biosigner.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/biosigner). 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/biosigner.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/biosigner).
7 7
8 ## Description 8 ### Description
9 9
10 **Version:** 2.2.4 10 **Version:** 2.2.6
11 **Date:** 2016-07-30 11 **Date:** 2016-08-05
12 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) 12 **Author:** Philippe Rinaudo and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) 13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
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. 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.
15 **Licence:** CeCILL 15 **Licence:** CeCILL
16 **Reference history:** [W4M00003_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published) 16 **Reference history:** [W4M00003_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published)
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) 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)
18 18
19 ## Installation 19 ### Installation
20 20
21 * Configuration file: `biosigner_config.xml`. 21 * Configuration file: `biosigner_config.xml`
22 * Image files: 22 * Image files:
23 + `static/images/biosigner_workflowPositionImage.png`. 23 + `static/images/biosigner_workflowPositionImage.png`
24 + `static/images/biosigner_workingExampleImage.png`. 24 + `static/images/biosigner_workingExampleImage.png`
25 * Wrapper file: `biosigner_wrapper.R`. 25 * Wrapper file: `biosigner_wrapper.R`
26 * R packages 26 * R packages
27 + **batch** from CRAN: `install.packages("batch", dep=TRUE)`. 27 + **batch** from CRAN
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")`. 28
29 ```r
30 install.packages("batch", dep=TRUE)
31 ```
32 + **biosigner** from Bioconductor
33
34 ```r
35 source("http://www.bioconductor.org/biocLite.R")
36 biocLite("biosigner")
37 ```
29 38
30 ## Tests 39 ### Tests
31 40
32 The code in the wrapper can be tested by running the `tests/biosigner_tests.R` in R 41 The code in the wrapper can be tested by running the `runit/biosigner_runtests.R` R file
33 42
34 ## News 43 You will need to install **RUnit** package in order to make it run:
44 ```r
45 install.packages('RUnit', dependencies = TRUE)
46 ```
35 47
36 ## CHANGES IN VERSION 2.2.4 48 ### Working example
37 49
38 * Internal updates for planemo and travis validation 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)
51
52 ### News
53
54 ###### CHANGES IN VERSION 2.2.6
55
56 INTERNAL MODIFICATION
57
58 * Minor internal modifications
39 59
40 ## CHANGES IN VERSION 2.2.2 60 ###### CHANGES IN VERSION 2.2.4
61
62 INTERNAL MODIFICATION
63
64 * Internal updates for planemo and travis validation
65
66 ###### CHANGES IN VERSION 2.2.2
67
68 INTERNAL MODIFICATION
41 69
42 * 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) 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)
43 71
44 ## CHANGES IN VERSION 2.2.1 72 ###### CHANGES IN VERSION 2.2.1
73
74 NEW FEATURE
45 75
46 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0) 76 * Creation of the tool: with S3 versions of biosigner (< 1.0.0) and ropls (< 1.4.0)