Mercurial > repos > iuc > data_manager_fetch_busco

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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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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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1 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
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2 <description>dataset dowloader</description>
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2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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3 <macros>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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4 <token name="@TOOL_VERSION@">5.4.6</token>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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5 <token name="@VERSION_SUFFIX@">0</token>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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6 </macros>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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7 <requirements>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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9 </requirements>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
iuc
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10 <command detect_errors="exit_code"><![CDATA[
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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11 python '$__tool_directory__/data_manager.py'
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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12 --database '$lineage'
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13 --name $lineage+\$(date +'%Y-%m-%d-%H%M%S')
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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14 --json '$out_file'
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15 --version '@TOOL_VERSION@'
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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16 ]]></command>
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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17 <inputs>
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18 <param name="lineage" type="select" label="Select the lineage to be downloaded">
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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19 <option value="all">All</option>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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20 <option value="prokaryota">Prokaryota</option>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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21 <option value="eukaryota">Eukaryota</option>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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22 <option value="virus">Virus</option>
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23 </param>
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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24 </inputs>
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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25 <outputs>
2
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26 <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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27 </outputs>
2
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28 <tests>
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29 <test expect_num_outputs="1">
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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30 <param name="lineage" value="virus"/>
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31 <output name="out_file">
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32 <assert_contents>
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33 <has_text text="virus"/>
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34 <has_text text="5.4.6"/>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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35 </assert_contents>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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36 </output>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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37 </test>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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38 </tests>
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39 <help>This tool downloads the BUSCO databases.</help>
2b4526fdf7fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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40 <citations>
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41 <citation type="doi">10.1093/bioinformatics/btv351</citation>
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42 </citations>
0
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43 </tool>