Mercurial > repos > workflow4metabolomics > mzxmlshaper
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| author | workflow4metabolomics |
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| date | Mon, 07 Oct 2024 11:40:19 +0000 |
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| 1 # mzXML Shaper | |
| 2 | |
| 3 | |
| 4 Metadata | |
| 5 ----------- | |
| 6 | |
| 7 * **@name**: mz(X)ML Shaper | |
| 8 * **@galaxyID**: mzxmlshaper | |
| 9 * **@version**: 1.0.0 | |
| 10 * **@authors**: Original code: Quentin Ruin (Contractual engineer - PFEM - INRAE - MetaboHUB) - Maintainer: Melanie Petera (PFEM - INRAE - MetaboHUB) | |
| 11 * **@init date**: 2024, September | |
| 12 * **@main usage**: This tool enables the conversion netCDF, mzML or mzXML files into W4M's XCMS mz(X)ML supported file formats | |
| 13 | |
| 14 | |
| 15 Context | |
| 16 ----------- | |
| 17 | |
| 18 The tool was created to cope with unsupported file formats that may not be read by W4M's Galaxy XCMS. | |
| 19 | |
| 20 It can be used for any purpose necessitating standardized mzML or mzXML files, be it visualization in a third-party software, local workflows or W4M XCMS workflows. | |
| 21 | |
| 22 User interface is based on the Galaxy platform (homepage: https://galaxyproject.org/). It is an open, web-based platform for data intensive biomedical research. | |
| 23 Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses. | |
| 24 | |
| 25 | |
| 26 Configuration | |
| 27 ----------- | |
| 28 | |
| 29 ### Requirement: | |
| 30 * R software: version = 4.3.3 recommended | |
| 31 * bioconductor-msdata = 0.42.0 | |
| 32 * bioconductor-mzr = 2.36.0 | |
| 33 * r-w4mrutils = 1.0.0 | |
| 34 | |
| 35 Technical description | |
| 36 ----------- | |
| 37 | |
| 38 Main files: | |
| 39 | |
| 40 - mzXMLShaper.R: R function (core script) | |
| 41 - mzXMLShaper.xml: XML wrapper (interface for Galaxy) | |
| 42 - ko16.CDF: netCDF test file from faahKO Bioconductor package (https://www.bioconductor.org/packages/release/data/experiment/html/faahKO.html) | |
| 43 - ko16.mzml: ko.CDF file converted to mzML using mzR R package | |
| 44 - ko16.mzXml: ko.CDF file converted to mzXML using mzR R package | |
| 45 | |
| 46 Services provided | |
| 47 ----------- | |
| 48 | |
| 49 * Help and support: https://community.france-bioinformatique.fr/c/workflow4metabolomics/10 | |
| 50 | |
| 51 | |
| 52 | |
| 53 License | |
| 54 ----------- | |
| 55 | |
| 56 * GPL-3.0-or-later |