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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
author iuc
date Mon, 24 Apr 2023 12:26:46 +0000
parents 53eec20e8fb6
children
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1:15b97817550a 2:2b4526fdf7fb
1 <?xml version="1.0"?> 1 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
2 <tool id="busco_fetcher" name="Busco" tool_type="manage_data" version="1.0.0">
3 <description>dataset dowloader</description> 2 <description>dataset dowloader</description>
4 <command detect_errors="exit_code"> 3 <macros>
5 <![CDATA[ 4 <token name="@TOOL_VERSION@">5.4.6</token>
6 python '$__tool_directory__/data_manager.py' --out '${out_file}' 5 <token name="@VERSION_SUFFIX@">0</token>
7 --url 'http://busco.ezlab.org/datasets/${dataset}.tar.gz' 6 </macros>
8 --name '${dataset}' 7 <requirements>
9 ]]> 8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
10 </command> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 python '$__tool_directory__/data_manager.py'
12 --database '$lineage'
13 --name $lineage+\$(date +'%Y-%m-%d-%H%M%S')
14 --json '$out_file'
15 --version '@TOOL_VERSION@'
16 ]]></command>
11 <inputs> 17 <inputs>
12 <param name="dataset" type="select" label="Choose dataset to download"> 18 <param name="lineage" type="select" label="Select the lineage to be downloaded">
13 <option value="eukaryota_odb9">eukaryota</option> 19 <option value="all">All</option>
14 <option value="metazoa_odb9">metazoa</option> 20 <option value="prokaryota">Prokaryota</option>
15 <option value="nematoda_odb9">nematoda</option> 21 <option value="eukaryota">Eukaryota</option>
16 <option value="arthropoda_odb9">arthropoda</option> 22 <option value="virus">Virus</option>
17 <option value="insecta_odb9">insecta</option>
18 <option value="endopterygota_odb9">endopterygota</option>
19 <option value="hymenoptera_odb9">hymenoptera</option>
20 <option value="diptera_odb9">diptera</option>
21 <option value="vertebrata_odb9">vertebrata</option>
22 <option value="actinopterygii_odb9">actinopterygii</option>
23 <option value="tetrapoda_odb9">tetrapoda</option>
24 <option value="aves_odb9">aves</option>
25 <option value="mammalia_odb9">mammalia</option>
26 <option value="euarchontoglires_odb9">euarchontoglires</option>
27 <option value="laurasiatheria_odb9">laurasiatheria</option>
28 <option value="embryophyta_odb9">embryophyta</option>
29 <option value="protists_ensembl">protists</option>
30 <option value="alveolata_stramenophiles_ensembl">alveolata</option>
31 <option value="fungi_odb9">fungi</option>
32 <option value="microsporidia_odb9">microsporidia</option>
33 <option value="dikarya_odb9">dikarya</option>
34 <option value="ascomycota_odb9">ascomycota</option>
35 <option value="pezizomycotina_odb9">pezizomycotina</option>
36 <option value="eurotiomycetes_odb9">eurotiomycetes</option>
37 <option value="sordariomyceta_odb9">sordariomyceta</option>
38 <option value="saccharomyceta_odb9">saccharomyceta</option>
39 <option value="saccharomycetales_odb9">saccharomycetales</option>
40 <option value="basidiomycota_odb9">basidiomycota</option>
41 <option value="bacteria_odb9">bacteria</option>
42 <option value="proteobacteria_odb9">proteobacteria</option>
43 <option value="rhizobiales_odb9">rhizobiales</option>
44 <option value="betaproteobacteria_odb9">betaproteobacteria</option>
45 <option value="gammaproteobacteria_odb9">gammaproteobacteria</option>
46 <option value="enterobacteriales_odb9">enterobacteriales</option>
47 <option value="deltaepsilonsub_odb9">deltaepsilonsub</option>
48 <option value="actinobacteria_odb9">actinobacteria</option>
49 <option value="cyanobacteria_odb9">cyanobacteria</option>
50 <option value="firmicutes_odb9">firmicutes</option>
51 <option value="clostridia_odb9">clostridia</option>
52 <option value="lactobacillales_odb9">lactobacillales</option>
53 <option value="bacillales_odb9">bacillales</option>
54 <option value="bacteroidetes_odb9">bacteroidetes</option>
55 <option value="spirochaetes_odb9">spirochaetes</option>
56 <option value="tenericutes_odb9">tenericutes</option>
57 </param> 23 </param>
58 </inputs> 24 </inputs>
59 <outputs> 25 <outputs>
60 <data name="out_file" format="data_manager_json" /> 26 <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
61 </outputs> 27 </outputs>
28 <tests>
29 <test expect_num_outputs="1">
30 <param name="lineage" value="virus"/>
31 <output name="out_file">
32 <assert_contents>
33 <has_text text="virus"/>
34 <has_text text="5.4.6"/>
35 </assert_contents>
36 </output>
37 </test>
38 </tests>
39 <help>This tool downloads the BUSCO databases.</help>
40 <citations>
41 <citation type="doi">10.1093/bioinformatics/btv351</citation>
42 </citations>
62 </tool> 43 </tool>