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annotate test-data/test1_metadata_xcms_1.txt @ 2:eac0e6feb850 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
author recetox
date Mon, 17 Jan 2022 16:28:54 +0000
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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1 Raw mass spectrometry data were processed using an R based workflow for feature detection, retention time alignment, feature grouping, peak filling, feature clustering. XCMS(v.3.14.0)was used for feature detection and retention time alighment. Processing was performed using R(v.R Core Team 2021). Feature data was input as an xcms object with ramclustR parameter settings of st = 12.99 sr = 0.5 and maxt = 259.8.RAMClustR (version 1.2.2) was utilized to cluster features into spectra (Broeckling 2014). The feature similarity matrix was clustered using fastcluster package heirarchical clustering method using the average method. The dendrogram was cut using the cutreeDynamicTree function from the dynamicTreeCut package. Cutting parameters were set to minModuleSize = 2, hmax = 0.3, and deepSplit = FALSE.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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3 1041 features were collapsed into 174 spectra.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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5 (Broeckling 2014): Broeckling CD, Afsar FA, Neumann S, Ben-Hur A, Prenni JE. RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data. Anal Chem. 2014. 86(14):6812-7.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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7 R Core Team: R Core Team (2021). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/.
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
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9 R Core Team (2021). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/.