Mercurial > repos > recetox > october_recetox_xmsannotator_advanced

comparison october_recetox_xmsannotator_advanced.xml @ 11:c6800346a5a8 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 330dd8c8be0c43b5ce38d8c5573325b2c555491d"
author recetox
date Wed, 03 Nov 2021 10:54:00 +0000
parents bdfd650ee1ab
children c1f439401578
comparison
equal deleted inserted replaced
10:a48e50d1dba3 11:c6800346a5a8
15 15
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("${adduct_table}"),
21 adduct_weights = as.data.frame(read.csv("${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($clustering.min_cluster_size),
27 deep_split = as.integer($clustering.deep_split), 27 deep_split = as.integer($clustering.deep_split),
28 network_type = "$clustering.network_type", 28 network_type = "$clustering.network_type",
29 ## #if $scoring.expected_adducts
30 ## expected_adducts = load_expected_adducts_csv("${scoring.expected_adducts}"),
31 ## #end if
32 ## #if $scoring.boost_compounds
33 ## boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
34 ## #end if
35 redundancy_filtering = $scoring.redundancy_filtering, 29 redundancy_filtering = $scoring.redundancy_filtering,
36 n_workers = n_workers, 30 n_workers = n_workers,
37 ## new params
38 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance), 31 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance),
39 mass_defect_tolerance = as.double($mass_defect_tolerance), 32 mass_defect_tolerance = as.double($mass_defect_tolerance),
40 mass_defect_precision = as.double($mass_defect_precision), 33 mass_defect_precision = as.double($mass_defect_precision),
41 peak_rt_width = as.integer($peak_rt_width), 34 peak_rt_width = as.integer($peak_rt_width),
42 maximum_isotopes = as.integer($maximum_isotopes), 35 maximum_isotopes = as.integer($maximum_isotopes),
43 min_ions_per_chemical = as.integer($min_ions_per_chemical), 36 min_ions_per_chemical = as.integer($min_ions_per_chemical),
44 filter_by = "$filter_by" 37 filter_by = "$filter_by"
45 ) 38 )
46
47 save_parquet(data = annotation, file = "${annotation_parquet}") 39 save_parquet(data = annotation, file = "${annotation_parquet}")
48 ]]></configfile> 40 ]]></configfile>
49 </configfiles> 41 </configfiles>
50 42
51 <inputs> 43 <inputs>
57 Retention time tolerance in seconds for finding peaks derived from the same parent compound. 49 Retention time tolerance in seconds for finding peaks derived from the same parent compound.
58 </help> 50 </help>
59 </param> 51 </param>
60 </expand> 52 </expand>
61 <section name="clustering" title="Clustering"> 53 <section name="clustering" title="Clustering">
62 <param name="correlation_method" type="select" display="radio" label="Correlation method">
63 <option value="pearson" selected="true"/>
64 <option value="spearman"/>
65 </param>
66 <param name="correlation_threshold" type="float" value="0.7"> 54 <param name="correlation_threshold" type="float" value="0.7">
67 <label>Correlation threshold</label> 55 <label>Correlation threshold</label>
68 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help> 56 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help>
69 </param> 57 </param>
70 <param name="min_cluster_size" type="integer" value="10" min="1"> 58 <param name="min_cluster_size" type="integer" value="10" min="1">
82 <label>Network type</label> 70 <label>Network type</label>
83 <help> 71 <help>
84 Network type parameter affects how the network's adjacency matrix is created from the correlation 72 Network type parameter affects how the network's adjacency matrix is created from the correlation
85 matrix (see WGCNA package documentation). 73 matrix (see WGCNA package documentation).
86 </help> 74 </help>
87 <option value="signed"/> 75 <option value="signed">Signed</option>
88 <option value="unsigned" selected="true"/> 76 <option value="unsigned" selected="true">Unsigned</option>
89 </param> 77 </param>
90 </section> 78 </section>
91 <section name="scoring" title="Scoring" expanded="true"> 79 <section name="scoring" title="Scoring" expanded="true">
92 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"> 80 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE">
93 <label>Strict boosting</label> 81 <label>Strict boosting</label>
94 <help> 82 <help>
95 Boost the scores of metabolites that not only belongs to the same pathway but also to the same 83 Boost the scores of metabolites that not only belongs to the same pathway but also to the same
96 cluster. Otherwise, do not account for cluster membership. 84 cluster. Otherwise, do not account for cluster membership.
97 </help> 85 </help>
98 </param> 86 </param>
99 <!-- <param name="expected_adducts" type="data" format="csv" optional="true">
100 <label>Expected adducts (optional)</label>
101
102 <help>
103 Require the presence of certain adducts for a high confidence match. By default, at least the
104 presence of an M+H adduct is required for a high confidence match.
105 </help>
106 </param> -->
107 <!-- <param name="boost_compounds" type="data" format="csv" optional="true">
108 <label>Validated compounds score boosting (optional)</label>
109 <help>
110 Table of previously validated compounds to boost their scores and confidence levels.
111 The 1st column of the table must contain IDs of compounds.
112 The optional 2nd and 3rd columns may contain mz values and retention times.
113 </help>
114 </param> -->
115 <param name="min_isp" type="integer" min="0" value="1"> 87 <param name="min_isp" type="integer" min="0" value="1">
116 <label>Minimum number of expected isotopes</label> 88 <label>Minimum number of expected isotopes</label>
117 <help> 89 <help>
118 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match. 90 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match.
119 </help> 91 </help>