Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_databases.xml @ 9:db4c810682ee draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 00d1775d87af54665ec1871f021bcec6b4b7a15a"
author iuc
date Tue, 24 Nov 2020 07:27:05 +0000
parents fbb459120c29
children
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fbb459120c29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
iuc
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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.3.1t" tool_type="manage_data" profile="18.09">
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iuc
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2 <description>Read the list of available SnpEff databases</description>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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3 <requirements>
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fbb459120c29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
iuc
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4 <requirement type="package" version="4.3.1t">snpeff</requirement>
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a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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5 </requirements>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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6 <command detect_errors="exit_code"><![CDATA[
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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7 python '$__tool_directory__/data_manager_snpEff_databases.py' '$out_file'
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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8 ]]></command>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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9 <inputs>
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iuc
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10 </inputs>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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11 <outputs>
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iuc
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12 <data name="out_file" format="data_manager_json"/>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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13 </outputs>
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iuc
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14 <tests>
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iuc
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15 <test>
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16 <output name="out_file">
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17 <assert_contents>
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18 <!-- Check that a genome was added -->
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fbb459120c29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
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19 <has_text text="GRCh38.86" />
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20 </assert_contents>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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21 </output>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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22 </test>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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23 </tests>
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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24 <help><![CDATA[
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25 This tool updates the list of SnpEff databases for the SnpEff Download data manager.
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
iuc
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26 It should only need to be run once for a SnpEff version, since it populates the SnpEff Download data manager from the SnpEff config file.
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27
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28 For information about SnpEff: http://snpeff.sourceforge.net
a9cace1ee2b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
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29 ]]></help>
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30 <citations>
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31 <citation type="doi">10.4161/fly.19695</citation>
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32 </citations>
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33 </tool>