Mercurial > repos > ethevenot > qualitymetrics
diff README.md @ 0:b4f5b5bc01dd draft
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
author | ethevenot |
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date | Sat, 06 Aug 2016 12:01:17 -0400 |
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children | 6d3b7b6573d8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Aug 06 12:01:17 2016 -0400 @@ -0,0 +1,73 @@ +Metrics and graphics to assess the quality of the data +====================================================== + +A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure + +Status: [](https://travis-ci.org/workflow4metabolomics/qualitymetrics). + +### Description + +**Version:** 2.2.4 +**Date:** 2016-08-04 +**Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST) +**Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) +**Citation:** +**Licence:** CeCILL +**Reference history:** [W4M00001b_sacurine-complete](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 + +* Configuration file: + + `qualitymetrics_config.xml` +* Image files: + + `static/images/QualityControl.png` + + `static/images/qualitymetrics_workingExampleImage.png` +* Wrapper file: + + `qualitymetrics_wrapper.R` +* Script file: + + `qualitymetrics_script.R` +* R packages + + **batch** from CRAN + + ```r + install.packages("batch", dep=TRUE) + ``` + + + **ropls** from Bioconductor + + ```r + source("http://www.bioconductor.org/biocLite.R") + biocLite("ropls") + ``` + +### Tests + +The code in the wrapper can be tested by running the `runit/qualitymetrics_runtests.R` R file + +You will need to install **RUnit** package in order to make it run: +```r +install.packages('RUnit', dependencies = TRUE) +``` + +### News + +##### CHANGES IN VERSION 2.2.4 + +INTERNAL MODIFICATION + + * Additional running and installation tests added with planemo, conda, and travis + +##### CHANGES IN VERSION 2.2.3 + +INTERNAL MODIFICATION + + * Modifications of the 'qualitymetrics_script.R' file to handle the recent 'ropls' package versions (i.e. 1.3.15 and above) which use S4 classes + + * Creating tests for the R code + +##### CHANGES IN VERSION 2.2.2 + +INTERNAL MODIFICATION + + * Minor internal modification