Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

comparison october_recetox_xmsannotator_advanced.xml @ 8:bdfd650ee1ab draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit c3738524c2032daec3acb8b2d4fcbbc8abf1b5de"
author recetox
date Mon, 01 Nov 2021 14:53:29 +0000
parents a762961e2251
children c6800346a5a8
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7:9b818895ff94 8:bdfd650ee1ab
16 annotation <- advanced_annotation( 16 annotation <- advanced_annotation(
17 #if $peak_table.is_of_type("parquet") 17 #if $peak_table.is_of_type("parquet")
18 peak_table = load_peak_table_parquet("${peak_table}"), 18 peak_table = load_peak_table_parquet("${peak_table}"),
19 #end if 19 #end if
20 ## adduct_table = load_adduct_table_parquet("${adduct_table}"), 20 ## adduct_table = load_adduct_table_parquet("${adduct_table}"),
21 adduct_weights = as.data.frame("${adduct_weights}"), 21 adduct_weights = as.data.frame(read.csv("${adduct_weights}")),
22 compound_table = load_compound_table_parquet("${compound_table}"), 22 compound_table = load_compound_table_parquet("${compound_table}"),
23 mass_tolerance = 1e-6 * ${mass_tolerance_ppm}, 23 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
24 time_tolerance = $time_tolerance, 24 time_tolerance = $time_tolerance,
25 correlation_threshold = as.double($clustering.correlation_threshold), 25 correlation_threshold = as.double($clustering.correlation_threshold),
26 min_cluster_size = as.integer($clustering.min_cluster_size), 26 min_cluster_size = as.integer($clustering.min_cluster_size),