Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

comparison october_recetox_xmsannotator_advanced.xml @ 1:8fcf5ca25f5d draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b26a7ce6459f8e456fd166ba1aaada4e7e66dfa6"
author recetox
date Fri, 29 Oct 2021 12:24:44 +0000
parents e2e2e455fcfb
children 116ec7c1c038
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0:e2e2e455fcfb 1:8fcf5ca25f5d
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 compound_table = load_compound_table_parquet("${compound_table}"), 22 compound_table = load_compound_table_parquet("${compound_table}"),
22 mass_tolerance = 1e-6 * ${mass_tolerance_ppm}, 23 mass_tolerance = 1e-6 * ${mass_tolerance_ppm},
23 time_tolerance = $time_tolerance, 24 time_tolerance = $time_tolerance,
24 correlation_threshold = as.double($clustering.correlation_threshold), 25 correlation_threshold = as.double($clustering.correlation_threshold),
25 min_cluster_size = as.integer($clustering.min_cluster_size), 26 min_cluster_size = as.integer($clustering.min_cluster_size),
52 <expand macro="tolerance"> 53 <expand macro="tolerance">
53 <param name="time_tolerance" type="float" value="10" min="0"> 54 <param name="time_tolerance" type="float" value="10" min="0">
54 <label>Retention time tolerance [s]</label> 55 <label>Retention time tolerance [s]</label>
55 <help> 56 <help>
56 Retention time tolerance in seconds for finding peaks derived from the same parent compound. 57 Retention time tolerance in seconds for finding peaks derived from the same parent compound.
57
58 </help> 58 </help>
59 </param> 59 </param>
60 </expand> 60 </expand>
61 <section name="clustering" title="Clustering"> 61 <section name="clustering" title="Clustering">
62 <param name="correlation_method" type="select" display="radio" label="Correlation method"> 62 <param name="correlation_method" type="select" display="radio" label="Correlation method">