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comparison data_manager/omamer.xml @ 0:d28438704310 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
author iuc
date Wed, 14 Aug 2024 15:42:38 +0000
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1 <tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
2 <macros>
3 <import>macros.xml</import>
4 </macros>
5 <version_command></version_command>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/omamer.py'
8 --name '$name'
9 --json '$output_file'
10 --version '@TOOL_VERSION@'
11 ]]></command>
12 <inputs>
13 <param name="output_dir" type="text" label="Output Directory" value=""/>
14 <param name="name" type="select" label="Database">
15 <option value="Primates_v2.0.0">Primates_v2.0.0</option>
16 <option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option>
17 <option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option>
18 <option value="LUCA_v0.2.5">LUCA_v0.2.5</option>
19 <option value="LUCA_v2.0.0">LUCA_v2.0.0</option>
20 <option value="Saccharomyceta">Saccharomyceta</option>
21 <option value="Homininae">Homininae</option>
22 </param>
23 </inputs>
24
25 <outputs>
26 <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/>
27 </outputs>
28
29 <tests>
30 <test>
31 <param name="output_dir" value="test_galaxy"/>
32 <param name="name" value="Primates_v2.0.0"/>
33 <output name="output_file" file="out.json"/>
34 </test>
35 </tests>
36
37 <help><![CDATA[
38 This data manager retrieves data from various pre-built databases.
39
40 .. _omamer: https://github.com/DessimozLab/omamer
41 ]]></help>
42 <citations>
43 <citation type="doi">10.1093/bioinformatics/btab219</citation>
44 </citations>
45 </tool>