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planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
author eschen42
date Sun, 29 Oct 2017 09:41:21 -0400
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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1 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1038289.svg)](https://doi.org/10.5281/zenodo.1038289)
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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3 # w4mjoinpn_galaxy_wrapper
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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5 This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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6 ionization-mode and the other in negative ionization-mode, for reasons set forth below.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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8 Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, http://dx.doi.org/10.1093/bioinformatics/btu813; http://workflow4metabolomics.org;
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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9 https://github.com/workflow4metabolomics) provides a suite of Galaxy tools for processing and analyzing metabolomics data.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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11 W4M uses the XCMS package (Smith *et al.*, 2006 http://dx.doi.org/10.1021/ac051437y) to extract features and align
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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12 their retention times among multiple samples.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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14 After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012, http://dx.doi.org/10.1021/ac202450g)
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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15 "to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum."
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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17 Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive)
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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18 because it would not make sense to attempt to use CAMERA otherwise.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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20 However, multivariate analysis in general, and particularly the "False Discovery Rate" adjustment in hypothesis testing,
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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21 would both benefit from having all variables (features), negative and positive, combined for one analysis. It is also
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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22 cumbersome to be forced to do an analysis twice, once for each ionization mode.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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24 This tool will fail:
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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25 * when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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26 * when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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28 Otherwise
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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29 * the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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30 are prefixed with "P"; negative, with "N".
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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31 * the two variableMetadata files are concatenated, and the names of features are prefixed in the same way.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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32 * if sampleMetadata has a polarity column, its value is set to "posneg" in the output.
05c964a1e589 planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
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33 * Technically, the sampleMetadata file in the output is derived from the negative ionization-mode sampleMetadata.