Mercurial > repos > recetox > recetox_xmsannotator_advanced
comparison recetox_xmsannotator_advanced.xml @ 0:cfd2e19f00a9 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 1ab1a1dabfcebe11720de1411927a7438c1b64c1
author | recetox |
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date | Mon, 26 Jun 2023 13:55:56 +0000 |
parents | |
children | 50ac7359ffe7 |
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1 <tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy0"> | |
2 | |
3 <description>annotate peak intensity table including scores and confidence levels</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="creator"/> | |
8 <xrefs> | |
9 <xref type="bio.tools">recetox-xmsannotator</xref> | |
10 </xrefs> | |
11 <expand macro="requirements" /> | |
12 <command detect_errors="aggressive"><![CDATA[ | |
13 Rscript -e 'source("${__tool_directory__}/utils.R")' -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')" | |
14 ]]></command> | |
15 | |
16 <configfiles> | |
17 <configfile name="wrapper"><![CDATA[ | |
18 metadata_table <- load_table("$metadata_table", "$metadata_table.ext") | |
19 intensity_table <- load_table("$intensity_table", "$intensity_table.ext") | |
20 peak_table <- create_peak_table(metadata_table, intensity_table) | |
21 | |
22 filter_by <- create_filter_by_adducts("$filter_by") | |
23 | |
24 annotation <- advanced_annotation( | |
25 peak_table = peak_table, | |
26 adduct_table = load_table("$adduct_table", "$adduct_table.ext"), | |
27 adduct_weights = load_table("$adduct_weights", "$adduct_weights.ext"), | |
28 compound_table = load_table("$compound_table", "$compound_table.ext"), | |
29 mass_tolerance = 1e-6 * ${mass_tolerance_ppm}, | |
30 time_tolerance = $time_tolerance, | |
31 correlation_threshold = as.double($clustering.correlation_threshold), | |
32 min_cluster_size = as.integer($clustering.min_cluster_size), | |
33 deep_split = as.integer($clustering.deep_split), | |
34 network_type = "$clustering.network_type", | |
35 redundancy_filtering = $scoring.redundancy_filtering, | |
36 n_workers = n_workers, | |
37 intensity_deviation_tolerance = as.double($intensity_deviation_tolerance), | |
38 mass_defect_tolerance = as.double($mass_defect_tolerance), | |
39 mass_defect_precision = as.double($mass_defect_precision), | |
40 peak_rt_width = as.integer($peak_rt_width), | |
41 maximum_isotopes = as.integer($maximum_isotopes), | |
42 min_ions_per_chemical = as.integer($min_ions_per_chemical), | |
43 filter_by = filter_by | |
44 ) | |
45 | |
46 save_table(annotation, "$output_file", "$output_file.ext") | |
47 ]]></configfile> | |
48 </configfiles> | |
49 | |
50 <inputs> | |
51 <expand macro="inputs"/> | |
52 <expand macro="tolerance"> | |
53 <param name="time_tolerance" type="float" value="10" min="0"> | |
54 <label>Retention time tolerance [s]</label> | |
55 <help> | |
56 Retention time tolerance in seconds for finding peaks derived from the same parent compound. | |
57 </help> | |
58 </param> | |
59 </expand> | |
60 <section name="clustering" title="Clustering"> | |
61 <param name="correlation_threshold" type="float" value="0.7"> | |
62 <label>Correlation threshold</label> | |
63 <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help> | |
64 </param> | |
65 <param name="min_cluster_size" type="integer" value="10" min="1"> | |
66 <label>Minimum cluster size</label> | |
67 <help>The minimum number of nodes to be considered as a cluster.</help> | |
68 </param> | |
69 <param name="deep_split" type="integer" value="2" min="0" max="4"> | |
70 <label>Deep split</label> | |
71 <help> | |
72 Deep split provides a rough control over sensitivity to cluster splitting. The higher the value, | |
73 the more and smaller clusters will be produced (see WGCNA package documentation). | |
74 </help> | |
75 </param> | |
76 <param name="network_type" type="select" display="radio"> | |
77 <label>Network type</label> | |
78 <help> | |
79 Network type parameter affects how the network's adjacency matrix is created from the correlation | |
80 matrix (see WGCNA package documentation). | |
81 </help> | |
82 <option value="signed">Signed</option> | |
83 <option value="unsigned" selected="true">Unsigned</option> | |
84 </param> | |
85 </section> | |
86 <section name="scoring" title="Scoring" expanded="true"> | |
87 <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"> | |
88 <label>Strict boosting</label> | |
89 <help> | |
90 Boost the scores of metabolites that not only belongs to the same pathway but also to the same | |
91 cluster. Otherwise, do not account for cluster membership. | |
92 </help> | |
93 </param> | |
94 <param name="min_isp" type="integer" min="0" value="1"> | |
95 <label>Minimum number of expected isotopes</label> | |
96 <help> | |
97 Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match. | |
98 </help> | |
99 </param> | |
100 <param name="max_isp" type="integer" min="0" value="5"> | |
101 <label>Maximum number of expected isotopes</label> | |
102 <help> | |
103 Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match. | |
104 </help> | |
105 </param> | |
106 <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"> | |
107 <label>Redundancy filtering</label> | |
108 <help>Whether to filter out low-scored multiple matcher or not.</help> | |
109 </param> | |
110 </section> | |
111 <param name="intensity_deviation_tolerance" type="float" value="0.1"> | |
112 <label>Tolerance of intensity deviation</label> | |
113 <help>A numeric threshold by which an intensity ratio of two isotopic peaks may differ from their actual abundance ratio.</help> | |
114 </param> | |
115 <param name="mass_defect_tolerance" type="float" value="0.1"> | |
116 <label>Tolerance of mass defect</label> | |
117 <help>Maximum difference in mass defect between two peaks of the same compound.</help> | |
118 </param> | |
119 <param name="mass_defect_precision" type="float" value="0.01"> | |
120 <label>Precision for computing mass defect</label> | |
121 </param> | |
122 <param name="peak_rt_width" type="integer" value="1"> | |
123 <label>Estimated chromatographic peak width</label> | |
124 </param> | |
125 <param name="maximum_isotopes" type="integer" value="10"> | |
126 <label>Maximum isotopes</label> | |
127 </param> | |
128 <param name="min_ions_per_chemical" type="integer" value="2"> | |
129 <label>Minimum ions per chemical</label> | |
130 </param> | |
131 <param name="filter_by" type="select" label="Adducts to filter by" multiple="true" optional="true"> | |
132 <option value="M-H" selected="true">M-H</option> | |
133 <option value="M+H" selected="true">M+H</option> | |
134 <option value="2M-H">2M-H</option> | |
135 <option value="M-2H">M-2H</option> | |
136 </param> | |
137 </inputs> | |
138 | |
139 <outputs> | |
140 <expand macro="outputs"/> | |
141 </outputs> | |
142 | |
143 <tests> | |
144 <test> | |
145 <param name="metadata_table" value="metadata_table.parquet" ftype="parquet" /> | |
146 <param name="intensity_table" value="intensity_table.parquet" ftype="parquet" /> | |
147 <param name="compound_table" value="database.parquet" ftype="parquet" /> | |
148 <param name="adduct_table" value="adduct_table.parquet" ftype="parquet" /> | |
149 <output name="output_file" file="expected_output.parquet" ftype="parquet"/> | |
150 </test> | |
151 <test> | |
152 <param name="metadata_table" value="metadata_table.csv" ftype="csv" /> | |
153 <param name="intensity_table" value="intensity_table.csv" ftype="csv" /> | |
154 <param name="compound_table" value="database.csv" ftype="csv" /> | |
155 <param name="adduct_table" value="adduct_table.csv" ftype="csv" /> | |
156 <output name="output_file" file="expected_output.csv" ftype="csv"/> | |
157 </test> | |
158 </tests> | |
159 | |
160 <help> | |
161 <![CDATA[ | |
162 @HELP@ | |
163 ]]> | |
164 </help> | |
165 | |
166 <citations> | |
167 <expand macro="citations"/> | |
168 </citations> | |
169 </tool> |