Mercurial > repos > recetox > xmsannotator_advanced

comparison xmsannotator_advanced.xml @ 4:6b2b2b83b46c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit c5151674ce7c552ad502d58089b8de93670d8e49"
author recetox
date Thu, 08 Oct 2020 08:01:18 +0000
parents 3bdef6d114fd
children 47185b5abe9e
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3:3bdef6d114fd 4:6b2b2b83b46c
14 Rscript -e 'annotation <- xmsannotator::advanced_annotation( 14 Rscript -e 'annotation <- xmsannotator::advanced_annotation(
15 peaks = xmsannotator::load_hdf("$peaks", "peaks"), 15 peaks = xmsannotator::load_hdf("$peaks", "peaks"),
16 adducts = xmsannotator::load_hdf("$adducts", "adducts"), 16 adducts = xmsannotator::load_hdf("$adducts", "adducts"),
17 compounds = xmsannotator::load_hdf("$compounds", "compounds"), 17 compounds = xmsannotator::load_hdf("$compounds", "compounds"),
18 18
19 mass_tolerance = 1e-6 * $mz_tolerance_ppm 19 mass_tolerance = 1e-6 * $mz_tolerance_ppm,
20 time_tolerance = $rt_tolerance, 20 time_tolerance = $rt_tolerance,
21 21
22 correlation_threshold = as.double($clustering.correlation_threshold), 22 correlation_threshold = as.double($clustering.correlation_threshold),
23 min_cluster_size = as.integer($clustering.min_cluster_size), 23 min_cluster_size = as.integer($clustering.min_cluster_size),
24 deep_split = as.integer($clustering.deep_split), 24 deep_split = as.integer($clustering.deep_split),