Mercurial > repos > workflow4metabolomics > mzxmlshaper

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
author workflow4metabolomics
date Mon, 07 Oct 2024 11:40:19 +0000
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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1 # mzXML Shaper
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4 Metadata
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5 -----------
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7 * **@name**: mz(X)ML Shaper
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8 * **@galaxyID**: mzxmlshaper
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9 * **@version**: 1.0.0
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10 * **@authors**: Original code: Quentin Ruin (Contractual engineer - PFEM - INRAE - MetaboHUB) - Maintainer: Melanie Petera (PFEM - INRAE - MetaboHUB)
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11 * **@init date**: 2024, September
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12 * **@main usage**: This tool enables the conversion netCDF, mzML or mzXML files into W4M's XCMS mz(X)ML supported file formats
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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15 Context
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16 -----------
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18 The tool was created to cope with unsupported file formats that may not be read by W4M's Galaxy XCMS.
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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.
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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.
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23 Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
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26 Configuration
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27 -----------
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29 ### Requirement:
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30 * R software: version = 4.3.3 recommended
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31 * bioconductor-msdata = 0.42.0
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32 * bioconductor-mzr = 2.36.0
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33 * r-w4mrutils = 1.0.0
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35 Technical description
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36 -----------
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38 Main files:
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40 - mzXMLShaper.R: R function (core script)
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41 - mzXMLShaper.xml: XML wrapper (interface for Galaxy)
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42 - ko16.CDF: netCDF test file from faahKO Bioconductor package (https://www.bioconductor.org/packages/release/data/experiment/html/faahKO.html)
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43 - ko16.mzml: ko.CDF file converted to mzML using mzR R package
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44 - ko16.mzXml: ko.CDF file converted to mzXML using mzR R package
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46 Services provided
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47 -----------
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49 * Help and support: https://community.france-bioinformatique.fr/c/workflow4metabolomics/10
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53 License
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54 -----------
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56 * GPL-3.0-or-later