Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.xml @ 10:c6fbc5421697 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
author iuc
date Sun, 22 Nov 2020 12:53:42 +0000
parents 08d7998c3afb
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08d7998c3afb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 036feef4f46b5aedabc5080c8fa4bc00d9c30d95"
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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3.1t" tool_type="manage_data" profile="18.09">
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2 <description>Download a new database</description>
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3 <requirements>
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4 <requirement type="package" version="4.3.1t">snpeff</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/data_manager_snpEff_download.py'
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8 --genome_version '$genome_version'
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9 '$out_file'
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10 ]]></command>
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11 <inputs>
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12 <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)" help="https://snpeff-data.galaxyproject.org/databases/">
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13 <validator type="regex" message="A genome version name is required">\S+</validator>
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14 </param>
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15 </inputs>
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17 <outputs>
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18 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="genome_version" value="GRCh38.86"/>
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23 <output name="out_file">
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24 <assert_contents>
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25 <!-- Check that a genome was added -->
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26 <has_text text="GRCh38.86" />
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27 <has_text text="snpeffv_regulationdb" />
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28 </assert_contents>
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29 </output>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb.
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34
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35 To see the list of available SnpEff genomes, run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeffv_databases.
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37 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
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38
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39 For details about this tool, please go to http://snpeff.sourceforge.net
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40 ]]></help>
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41 <citations>
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42 <citation type="doi">10.4161/fly.19695</citation>
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43 </citations>
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44 </tool>