Mercurial > repos > iuc > data_manager_fetch_busco

annotate data_manager/busco_options.xml @ 7:83c7f3907ad2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 68696449a909c43d0e44bc9cfc8f8945e8a9dfce
author iuc
date Fri, 04 Apr 2025 11:17:37 +0000
parents b2d2cba0dca6
children
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6
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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1 <tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">5.8.0</token>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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5 <token name="@VERSION_SUFFIX@">0</token>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
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9 </requirements>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $test:
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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12 busco --download_path test/ --download virus > /dev/null &&
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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13 #set db_path="./test"
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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14 #else
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15 #set db_path=$cached_db.fields.path
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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16 #end if
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17 python '$__tool_directory__/extract.py' '$db_path' '$cached_db' '$out_file'
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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18 ]]></command>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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19 <inputs>
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20 <param name="test" type="hidden"/>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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21 <param name="cached_db" label="Cached database with lineage" type="select">
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22 <options from_data_table="busco_database">
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23 <validator message="No BUSCO database is available" type="no_options"/>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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24 </options>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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25 </param>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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26 </inputs>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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27 <outputs>
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28 <data name="out_file" format="data_manager_json" label="BUSCO options data manager: JSON"/>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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29 </outputs>
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30 <tests>
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31 <test expect_num_outputs="1">
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32 <param name="test" value="true"/>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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33 <param name="cached_db" value="test"/>
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34 <output name="out_file">
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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35 <assert_contents>
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36 <has_text text="busco_database_options"/>
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37 <has_text text="Chordopoxvirinae"/>
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38 <has_text text="chordopoxvirinae_"/>
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39 </assert_contents>
b2d2cba0dca6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c
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40 </output>
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41 </test>
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42 </tests>
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43 <help>This tool determines the possible choices of BUSCO lineages in a given BUSCO DB.</help>
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44 <citations>
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45 <citation type="doi">10.1093/bioinformatics/btv351</citation>
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46 </citations>
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47 </tool>