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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
author workflow4metabolomics
date Tue, 29 Aug 2023 09:45:16 +0000
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1 <tool id="kmd_hmdb_data_plot" name="KMD HMDB Data Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>
3 retrieves data from KMD HMDB API and produce plot and tsv file
4 </description>
5 <macros>
6 <import>macro.xml</import>
7 <token name="@TOOL_VERSION@">1.0.0</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 </macros>
10 <edam_topics>
11 <edam_topic>topic_0091</edam_topic>
12 </edam_topics>
13 <edam_operations>
14 <edam_operation>operation_3803</edam_operation>
15 </edam_operations>
16 <requirements>
17 <requirement type="package" version="3.10">python</requirement>
18 <requirement type="package" version="2.0.3">pandas</requirement>
19 <requirement type="package" version="5.15.0">plotly</requirement>
20 <requirement type="package" version="1.0.1">kmd_hmdb_api_client</requirement>
21 </requirements>
22 <command detect_errors="exit_code">
23 <![CDATA[
24 #if "get_data" in str($what.to_do)
25 python3 '$__tool_directory__/kmd_hmdb_interrogator.py' compound
26 --mz-ratio '$what.mz_ratio'
27 --database '$what.database'
28 --mass-tolerance '$what.mass_tolerance'
29 #for adduct in $what.adducts
30 --adducts '$adduct'
31 #end for
32 --output-path '$output_path'
33 #end if
34
35 #if $what.to_do == "get_data_and_produce_plot"
36 &&
37 #end if
38
39 #if "produce_plot" in str($what.to_do)
40 python3 '$__tool_directory__/kmd_hmdb_plot_generator.py' plot
41
42 #if "get_data" in str($what.to_do)
43 --input '$output_path'
44 #else
45 --input '$what.tsv_input'
46 #end if
47
48 #if $what.x_columns
49 #for x in $what.x_columns
50 --x-column '$x'
51 #end for
52 #end if
53
54 #if $what.y_columns
55 #for y in $what.y_columns
56 --y-column '$y'
57 #end for
58 #end if
59
60 #if $what.annotation_columns
61 #for annotation_column in $what.annotation_columns
62 --annotation-column '$annotation_column'
63 #end for
64 #end if
65
66 --output 'out.html'
67
68 && cat 'out.html' > '$output'
69 #end if
70 ]]>
71 </command>
72
73 <inputs>
74 <conditional name="what">
75 <param name="to_do" type="select"
76 label="What to do"
77 >
78 <option value="get_data">Only get data</option>
79 <option value="produce_plot">Only produce plot</option>
80 <option value="get_data_and_produce_plot" selected="true">
81 Get data from database + Produce Plot
82 </option>
83 </param>
84 <when value="produce_plot">
85 <expand macro="produce_plot_inputs" />
86 <expand macro="not_get_data" />
87 </when>
88 <when value="get_data">
89 <expand macro="get_data_inputs" />
90 <expand macro="not_produce_plot" />
91 </when>
92 <when value="get_data_and_produce_plot">
93 <expand macro="get_data_inputs" />
94 <expand macro="not_produce_plot" />
95 </when>
96 </conditional>
97 </inputs>
98
99 <outputs>
100 <expand macro="get_data_outputs" />
101 <expand macro="produce_plot_outputs" />
102 </outputs>
103
104 <tests>
105 <test>
106 <!-- #1 get_data with tolerance = 0.01 -->
107 <param name="to_do" value="get_data" />
108 <param name="mass_tolerance" value="0.01" />
109 <param name="mz_ratio" value="303.05" />
110 <param name="database" value="hmdb" />
111 <param name="adducts" value="M+H" />
112 <output name="output_path" file="get_data_tol_0.01.tsv" />
113 </test>
114 </tests>
115
116 <help><![CDATA[
117
118 This tool includes two utilities.
119 One that retrieves data from the KMD HMDB API formated as a tsv file,
120 and the other plots those data in a plotly graph.
121
122 The default behavior of the plot is to produce a plot of the kmd in
123 in function of the nominal mass of the compound.
124
125 Compounds are retrieved using a query with default parameters:
126 - mz default to @DEFAULT_MZ@
127 - mz tolerance defaults to @DEFAULT_TOLERENCE@
128 - adduct list defaults to "@DEFAULT_ADDUCT@"
129 - database default to "@DEFAULT_DATABASE@", and possible values are one of:
130
131 - KMD Metabolites
132 - HMDB
133
134 Those two utilities are usable independently, or sequentially in galaxy.
135
136 Multiple X / Y values in the X/Y column selection can be
137 selected to produce a lot of graphs at once.
138
139 For example, imagine you have 5 columns in you tsv file,
140 and those columns are named: A, B, C, D and F.
141
142 If you choose X = [A, C] and Y = [B],
143 then you will get two graphs (in one single HTML file) with:
144
145 - f(A) = B
146 - f(C) = B
147
148 But if you choose multiple values for both X and Y, you get
149 all combinations of columns X and Y. For example, if you
150 select X = [A, B] and Y = [C, D, E], then you will get six
151 graphs on the same plot:
152
153 - f(A) = C
154 - f(A) = D
155 - f(A) = E
156 - f(B) = C
157 - f(B) = D
158 - f(B) = E
159
160 All those graph's traces will be tooglable in the HTML page.
161 So don't hesitate to select a lot of parameters for X and Y!
162
163 ]]>
164 </help>
165 <citations></citations>
166 <creator>
167 <person
168 honorificPrefix="Mx."
169 givenName="Lain"
170 familyName="Pavot"
171 email="lain.pavot@inrae.fr"
172 identifier="https://orcid.org/0009-0007-1841-4358"
173 />
174 </creator>
175
176 </tool>