Mercurial > repos > iuc > data_manager_snpeff

annotate data_manager/data_manager_snpEff_download.xml @ 4:a9cace1ee2b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1-dirty
author iuc
date Tue, 18 Apr 2017 09:39:00 -0400
parents 821c34cdacb6
children a6e6e8415b7f
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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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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.3k" tool_type="manage_data">
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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="4.3k">snpeff</requirement>
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821c34cdacb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
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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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111fc9457ec6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpeff commit 88c982c5adcd32b11d98428fc554a4fdfcc19584
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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="GRCh38.76"/>
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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="GRCh38.76" />
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27 <has_text text="snpeffv_regulationdb" />
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28 <has_text text="snpeffv_annotations" />
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 This tool downloads a SnpEff database and populates the data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
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36 To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases
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38 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
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39
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40 For details about this tool, please go to http://snpeff.sourceforge.net
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41 ]]></help>
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42 <citations>
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43 <citation type="doi">10.4161/fly.19695</citation>
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44 </citations>
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45 </tool>