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annotate snpEff_download.xml @ 22:bb0797deab78 draft

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author jjohnson
date Wed, 09 Dec 2015 10:20:13 -0500
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1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
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2 <description>Download a new database</description>
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3 <macros>
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4 <import>snpEff_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
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16 <help>@SNPEFF_DATABASE_URL@</help>
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17 <validator type="regex" message="A genome version name is required">\S+</validator>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
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22 </outputs>
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23 <help><![CDATA[
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25 @EXTERNAL_DOCUMENTATION@
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27 @CITATION_SECTION@
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29 ]]>
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30 </help>
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31 <expand macro="citations" />
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32 </tool>
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