Mercurial > repos > ethevenot > checkformat
comparison README.md @ 1:e194eec8e70c draft
planemo upload for repository https://github.com/workflow4metabolomics/checkformat.git commit 8ebfbfa8d9449c9bbfbf569851a30b1e33df0b3f
author | ethevenot |
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date | Sat, 06 Aug 2016 11:54:28 -0400 |
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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 *** |