Mercurial > repos > ethevenot > checkformat
comparison README.md @ 0:059eb452931e draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit e17f78630b4d21b54a4edd6015d50969ac859d6b
author | ethevenot |
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date | Tue, 24 Oct 2017 08:44:02 -0400 |
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1 Checking the formats of the dataMatrix, sampleMetadata, and variableMetadata files | |
2 ================================================================================== | |
3 | |
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure | |
5 | |
6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/checkformat.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/checkformat). | |
7 | |
8 ### Description | |
9 | |
10 **Version:** 2.0.4 | |
11 **Date:** 2016-07-29 | |
12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) | |
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) | |
14 **Citation:** Thevenot E.A., Roux A., Xu Y., Ezan E. and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335. [doi:10.1021/acs.jproteome.5b00354](http://dx.doi.org/10.1021/acs.jproteome.5b00354) | |
15 **Licence:** CeCILL | |
16 **Reference histories:** | |
17 [W4M00001a_sacurine-subset-statistics](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00001b_sacurine_complete](http://galaxy.workflow4metabolomics.org/history/list_published), | |
18 [W4M00002_sacurine_mtbls2](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00003_sacurine_diaplasma](http://galaxy.workflow4metabolomics.org/history/list_published) | |
19 **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) | |
20 | |
21 ### Installation | |
22 | |
23 * Configuration file: `checkformat_config.xml` | |
24 * Image file: `static/images/checkformat_workflowPositionImage.png` | |
25 * Wrapper file: `checkformat_wrapper.R` | |
26 * R packages | |
27 + **batch** from CRAN | |
28 | |
29 ```r | |
30 install.packages("batch", dep=TRUE) | |
31 ``` | |
32 | |
33 ### Tests | |
34 | |
35 The code in the wrapper can be tested by running the `runit/checkformat_tests.R` R file | |
36 | |
37 You will need to install **RUnit** package in order to make it run: | |
38 ```r | |
39 install.packages('RUnit', dependencies = TRUE) | |
40 ``` | |
41 | |
42 ### Working example | |
43 | |
44 See the **W4M00001a_sacurine-subset-statistics**, **W4M00001b_sacurine-complete**, **W4M00002_mtbls2**, or **W4M00003_diaplasma** shared histories in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published) | |
45 | |
46 ### News | |
47 | |
48 ##### CHANGES IN VERSION 2.0.4 | |
49 | |
50 INTERNAL MODIFICATION | |
51 | |
52 * Minor internal modifications | |
53 | |
54 ##### CHANGES IN VERSION 2.0.2 | |
55 | |
56 INTERNAL MODIFICATION | |
57 | |
58 * Creating tests for R code |