Mercurial > repos > workflow4metabolomics > kmd_hmdb_data_plot

comparison macro.xml @ 0:59c8bad5f6bc draft default tip

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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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comparison
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-1:000000000000 0:59c8bad5f6bc
1 <macros>
2
3 <token name="@DEFAULT_MZ@">303.05</token>
4 <token name="@DEFAULT_TOLERENCE@">10.0</token>
5 <token name="@DEFAULT_ADDUCT@">M+H</token>
6 <token name="@DEFAULT_DATABASE@">HMDB</token>
7
8 <xml name="get_data_inputs">
9 <param argument="--mz-ratio" type="float" min="1" max="1000" value="@DEFAULT_MZ@"
10 help="
11 The database will give us all compounds with m/z =
12 m/zRatio±MassTolerance and we will plot those
13 compounds.
14 Choose the mass tolerance according to this information.
15 "
16 label="M/z Ratio"
17 />
18
19 <param argument="--mass-tolerance" type="float" value="@DEFAULT_TOLERENCE@"
20 help="
21 The database will give us all compounds with m/z =
22 m/zRatio±MassTolerance and we will plot those
23 compounds.
24 Choose the mass tolerance according to this information.
25 "
26 label="Mass Tolerance"
27 />
28
29 <param argument="--database" type="select" value="@DEFAULT_DATABASE@"
30 label="Which database to interrogate"
31 help="
32 Those databases are sub-databases of KMD-HMDB Metabolites
33 and contains compounds with their KMD.
34 "
35 >
36 <option selected="true" value="hmdb">HMDB</option>
37 <option value="farid">KMD Metabolites</option>
38 </param>
39
40 <param argument="--adducts" type="select" multiple="true"
41 label="Adducts"
42 help="Which adducts to retrieve"
43 >
44 <option selected="true" value="M+H">M+H</option>
45 <option value="M+2H">M+2H</option>
46 <option value="M+H+NH4">M+H+NH4</option>
47 <option value="M+H+Na">M+H+Na</option>
48 <option value="M+H+K">M+H+K</option>
49 <option value="M+ACN+2H">M+ACN+2H</option>
50 <option value="M+2Na">M+2Na</option>
51 <option value="M+H-2H2O">M+H-2H2O</option>
52 <option value="M+H-H2O">M+H-H2O</option>
53 <option value="M+NH4">M+NH4</option>
54 <option value="M+Na">M+Na</option>
55 <option value="M+CH3OH+H">M+CH3OH+H</option>
56 <option value="M+K">M+K</option>
57 <option value="M+ACN+H">M+ACN+H</option>
58 <option value="M+2Na-H">M+2Na-H</option>
59 <option value="M+IsoProp+H">M+IsoProp+H</option>
60 <option value="M+ACN+Na">M+ACN+Na</option>
61 <option value="M+2K+H">M+2K+H</option>
62 <option value="M+DMSO+H">M+DMSO+H</option>
63 <option value="M+2ACN+H">M+2ACN+H</option>
64 <option value="2M+H">2M+H</option>
65 <option value="2M+NH4">2M+NH4</option>
66 <option value="2M+Na">2M+Na</option>
67 <option value="2M+K">2M+K</option>
68 <option value="M-H">M-H</option>
69 <option value="M-2H">M-2H</option>
70 <option value="M-H2O-H">M-H2O-H</option>
71 <option value="M+Cl">M+Cl</option>
72 <option value="M+FA-H">M+FA-H</option>
73 <option value="M+Hac-H">M+Hac-H</option>
74 <option value="M-H+HCOONa">M-H+HCOONa</option>
75 <option value="M+Br">M+Br</option>
76 <option value="M+TFA-H">M+TFA-H</option>
77 <option value="2M-H">2M-H</option>
78 <option value="2M+FA-H">2M+FA-H</option>
79 <option value="2M+Hac-H">2M+Hac-H</option>
80 </param>
81 </xml>
82
83 <xml name="produce_plot_inputs">
84 <param name="tsv_input" type="data" format="tsv"
85 help="Tabular file to use to produce the plot."
86 label="A Tabular Input File"
87 />
88 <param
89 name="annotation_columns"
90 type="data_column"
91 data_ref="tsv_input"
92 use_header_names="true"
93 multiple="true"
94 optional="true"
95 help="Select columns to show when a point of the graph is hovered"
96 label="Annotation columns"
97 />
98 <param
99 name="x_columns"
100 type="data_column"
101 data_ref="tsv_input"
102 use_header_names="true"
103 optional="true"
104 multiple="true"
105 help="
106 Select one or multiple column to use as X values
107 to generate the graph. See the help section to better
108 understand the usage of multiple values
109 "
110 label="X Axis"
111 />
112 <param
113 name="y_columns"
114 type="data_column"
115 data_ref="tsv_input"
116 use_header_names="true"
117 optional="true"
118 multiple="true"
119 help="
120 Select one or multiple column to use as Y values
121 to generate the graph. See the help section to better
122 understand the usage of multiple values
123 "
124 label="Y Axis"
125 />
126 </xml>
127
128 <xml name="not_get_data">
129 <param name="mz_ratio" value="unknown" type="hidden" />
130 <param name="mass_tolerance" value="unknown" type="hidden" />
131 <param name="database" value="unknown" type="hidden" />
132 <param name="adducts" value="unknown" type="hidden" />
133 </xml>
134
135 <xml name="not_produce_plot">
136 <param name="tsv_input" value="unknown" type="hidden" />
137 <param name="annotation_columns" type="hidden" />
138 <param name="x_columns" type="hidden" />
139 <param name="y_columns" type="hidden" />
140 </xml>
141
142 <xml name="get_data_outputs">
143 <data name="output_path" format="tsv"
144 label="tsv - ${tool.name} on ${what.mz_ratio}±${what.mass_tolerance} - ${what.database}"
145 >
146 <filter>"get_data" in str(what['to_do'])</filter>
147 <actions>
148 <action name="column_names" type="metadata"
149 default="database,metabolite_name,chemical_formula,hmdb_id,inchikey,compound_id,adduct,kendricks_mass,kendricks_mass_defect,monisotopic_molecular_weight,nominal_mass,polarity,annotation_id"
150 />
151 </actions>
152 </data>
153 </xml>
154
155 <xml name="produce_plot_outputs">
156 <data name="output" format="html"
157 label="html - ${tool.name} on ${
158 ' - '
159 + str($what['mz_ratio'])
160 + '±' + str($what['mass_tolerance'])
161 + ' - ' + str($what['database'])
162 if 'get_data' in str($what['to_do'])
163 else ''' ' ''' + $what.csv_input.name + ''' ' '''
164 }"
165 >
166 <filter>"produce_plot" in str(what['to_do'])</filter>
167 </data>
168 </xml>
169
170 </macros>