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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/freqsap commit 202a898874d0de51b9923430ea0ef3040084c8d0
author recetox
date Fri, 18 Jul 2025 13:21:36 +0000
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1 <tool id="freqsap" name="freqSAP" version="1.0.0+galaxy0" profile="23.0" license="MIT">
2 <description>Get frequencies of single amino-acid polymorphisms based on nucleid-acid polymorphism for different populations from UniProt and DbSNP</description>
3
4 <creator>
5 <person
6 givenName="Helge"
7 familyName="Hecht"
8 url="https://github.com/hechth"
9 identifier="0000-0001-6744-996X" />
10 <organization
11 url="https://www.recetox.muni.cz/"
12 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
13 name="RECETOX MUNI" />
14 </creator>
15
16 <edam_topics>
17 <edam_topic>topic_0121</edam_topic>
18 <edam_topic>topic_3366</edam_topic>
19 </edam_topics>
20
21 <edam_operations>
22 <edam_operation>operation_3197</edam_operation>
23 <edam_operation>operation_2479</edam_operation>
24 <edam_operation>operation_2422</edam_operation>
25 </edam_operations>
26
27 <requirements>
28 <requirement type="package" version="2.3.0">pandas</requirement>
29 <requirement type="package" version="2.32.4">requests</requirement>
30 <requirement type="package" version="3.1.5">openpyxl</requirement>
31 </requirements>
32
33 <required_files>
34 <include path="freqSAP.py"/>
35 </required_files>
36
37 <command detect_errors="exit_code"><![CDATA[
38 python3 '${__tool_directory__}/freqSAP.py' -a '$accession' -p '$populations' -f '$output_format' -o '$output_file'
39 ]]></command>
40 <inputs>
41 <param argument="--accession" type="text" label="Protein Accession in UniProt" help="UniProt accession of the protein to fetch variation data for.">
42 <sanitizer invalid_char="">
43 <valid initial="string.letters,string.digits">
44 <add value="_" />
45 </valid>
46 </sanitizer>
47 <validator type="regex">[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}</validator>
48 </param>
49 <param argument="--populations" type="select" multiple="true" optional="false" label="Regions from which to choose the populations" help="The regions are broken down into sub-populations based on available entries in DbSNP.">
50 <option value="Africa">Africa</option>
51 <option value="North America">North America</option>
52 <option value="Asia">Asia</option>
53 <option value="Europe">Europe</option>
54 <option value="South America">South America</option>
55 <option value="Middle East">Middle East</option>
56 <option value="Other">Other</option>
57 <option value="Global" selected="true">Global</option>
58 </param>
59 <param argument="--output_format" type="select" label="Output Format" help="Format in which to store the output file.">
60 <option value="tabular" selected="true">Tab Separated Value (tabular)</option>
61 <option value="csv">Comma Separated Value (csv)</option>
62 <option value="xlsx">Excel (xlsx)</option>
63 </param>
64 </inputs>
65 <outputs>
66 <data name="output_file" format="tabular" label="${tool.name} of ${accession}">
67 <change_format>
68 <when input="output_format" value="xlsx" format="xlsx"/>
69 <when input="output_format" value="csv" format="csv"/>
70 </change_format>
71 </data>
72 </outputs>
73
74 <tests>
75 <test>
76 <param name="accession" value="P0DJI9"/>
77 <param name="populations" value="Europe,Asia"/>
78 <output name="output_file" ftype="tabular">
79 <assert_contents>
80 <has_n_columns n="21"/>
81 <has_n_lines n="807" delta="20"/>
82 <has_text text="rs1044068853"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <param name="accession" value="P05067"/>
88 <param name="populations" value="Global"/>
89 <param name="output_format" value="xlsx"/>
90 <output name="output_file" ftype="xlsx">
91 <assert_contents>
92 <has_size size="161" delta="10"/>
93 </assert_contents>
94 </output>
95 </test>
96 </tests>
97
98 <help><![CDATA[
99 freqSAP: Frequency of Single Amino-Acid Polymorphisms
100 =====================================================
101
102 This tool retrieves the frequencies of single amino-acid polymorphisms (SAPs) for a given protein accession from UniProt and DbSNP, broken down by population regions.
103
104 Inputs
105 ------
106
107 - **Protein Accession in UniProt:**
108 Enter the UniProt accession (e.g., ``P12345``) for the protein of interest.
109
110 - **Regions from which to choose the populations:**
111 Select one or more population regions. The tool will fetch SAP frequencies for the selected regions.
112
113 - **Output Format:**
114 Choose the format for the output file:
115
116 - Tab Separated Value (``tabular``)
117 - Comma Separated Value (``csv``)
118 - Excel (``xlsx``)
119
120 Outputs
121 -------
122
123 - A table listing SAP frequencies for the selected protein and populations, in the chosen format.
124
125 Example Usage
126 -------------
127
128 1. Enter a UniProt accession (e.g., ``P69905``).
129 2. Select ``Europe`` and ``Asia`` as populations.
130 3. Choose ``csv`` as the output format.
131 4. Run the tool to download the SAP frequency table.
132 ]]></help>
133
134 <citations>
135 <citation type="doi">10.1093/nar/29.1.308</citation>
136 <citation type="doi">10.1093/nar/gkaf394</citation>
137 </citations>
138 </tool>