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planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
author ethevenot
date Sat, 06 Aug 2016 11:54:28 -0400
parents 0d8099822c49
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1 ## Checking the formats of the dataMatrix, sampleMetadata, and variableMetadata files 1 Checking the formats of the dataMatrix, sampleMetadata, and variableMetadata files
2 #### A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) project 2 ==================================================================================
3
4 A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure
3 5
4 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/checkformat.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/checkformat). 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/checkformat.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/checkformat).
5 7
6 ### Description 8 ### Description
7 9
8 **Version:** 2.0.2 10 **Version:** 2.0.4
9 **Date:** 2016-07-29 11 **Date:** 2016-07-29
10 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) 12 **Author:** Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
11 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) 13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
12 **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) 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)
13 **Licence:** CeCILL 15 **Licence:** CeCILL
16 [W4M00002_sacurine_mtbls2](http://galaxy.workflow4metabolomics.org/history/list_published), [W4M00003_sacurine_diaplasma](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)
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) 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)
18 20
19 ### Installation 21 ### Installation
20 22
21 * Configuration file: **checkFormat_config.xml** 23 * Configuration file: `checkformat_config.xml`
22 * Image file: **static/images/checkFormat_workflowPositionImage.png** 24 * Image file: `static/images/checkformat_workflowPositionImage.png`
23 * Wrapper file: **checkFormat_wrapper.R** 25 * Wrapper file: `checkformat_wrapper.R`
24 * R packages 26 * R packages
25 + **batch** from CRAN 27 + **batch** from CRAN
26 > install.packages("batch", dep=TRUE) 28
29 ```r
30 install.packages("batch", dep=TRUE)
31 ```
27 32
28 ### Tests 33 ### Tests
29 34
30 The code in the wrapper can be tested by running the **tests/checkFormat_tests.R** in R 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)
31 45
32 ### News 46 ### News
47
48 ##### CHANGES IN VERSION 2.0.4
49
50 INTERNAL MODIFICATION
51
52 * Minor internal modifications
33 53
34 ##### CHANGES IN VERSION 2.0.2 54 ##### CHANGES IN VERSION 2.0.2
35 55
36 INTERNAL MODIFICATION 56 INTERNAL MODIFICATION
37 57
38 o Creating tests for R code 58 * Creating tests for R code
39
40 ***