Mercurial > repos > melpetera > idchoice
comparison IDchoice/README.md @ 0:b7a6a88f518a draft
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| author | melpetera |
|---|---|
| date | Thu, 11 Oct 2018 05:47:29 -0400 |
| parents | |
| children | bb19b1d15732 |
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| 1 ID choice | |
| 2 ======= | |
| 3 | |
| 4 Metadata | |
| 5 ----------- | |
| 6 | |
| 7 * **@name**: ID choice | |
| 8 * **@version**: 17.11 | |
| 9 * **@authors**: Melanie Petera - PFEM ; INRA ; MetaboHUB | |
| 10 * **@init date**: 2017/06/07 | |
| 11 * **@main usage**: This tool is designed to make you choose a particular column in your metadata file to be considered as identifiers for your W4M-3-tables-format data. | |
| 12 | |
| 13 | |
| 14 Context | |
| 15 ----------- | |
| 16 | |
| 17 This tool is one of the [Workflow4Metabolomics](http://workflow4metabolomics.org) Galaxy instance utilities. W4M is a French infrastructure providing software tools to process, analyse and annotate metabolomics data. | |
| 18 | |
| 19 User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | |
| 20 | |
| 21 | |
| 22 Configuration | |
| 23 ----------- | |
| 24 | |
| 25 ### Requirement: | |
| 26 * R software: version > 3.0.0 recommended | |
| 27 * Specific R library: 'batch' | |
| 28 * Submodule: [easyRlibrary](https://github.com/workflow4metabolomics/easyrlibrary-lib) (Required for internal input quality checks) | |
| 29 | |
| 30 ### Deploy: | |
| 31 * [get project data](https://github.com/workflow4metabolomics/idchoice) | |
| 32 * How to get the submodule files: | |
| 33 When pulling this module's Git repository, you may only obtain an empty folder for the needed submodule. | |
| 34 You can initialise it then with the following command: | |
| 35 ```bash | |
| 36 git submodule update --init --recursive | |
| 37 ``` | |
| 38 | |
| 39 | |
| 40 Travis test | |
| 41 ----------- | |
| 42 | |
| 43 [](https://travis-ci.org/workflow4metabolomics/idchoice) | |
| 44 Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes! | |
| 45 | |
| 46 | |
| 47 Technical description | |
| 48 ----------- | |
| 49 | |
| 50 Main files: | |
| 51 | |
| 52 - IDchoice_script.R: R function (core script) | |
| 53 - IDchoice_wrap.R: R script to link the main R function to inputs | |
| 54 - IDchoice.xml: XML wrapper (interface for Galaxy) | |
| 55 | |
| 56 | |
| 57 Services provided | |
| 58 ----------- | |
| 59 | |
| 60 * Help and support: support@workflow4metabolomics.org |