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annotate snpEff_download.xml @ 19:2e37b58fc24d

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Fix some versions
author Jim Johnson <jj@umn.edu>
date Tue, 13 Jan 2015 15:01:37 -0600
parents 36f3c82323e6
children c780e3f75b3d
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36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
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1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.2">
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2 <description>Download a new database</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>snpEff_macros.xml</import>
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6 </macros>
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7 <command>
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8 <![CDATA[
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9 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version
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10 ]]>
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11 </command>
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12 <inputs>
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13 <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
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14 <help>@SNPEFF_DATABASE_URL@</help>
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15 <validator type="regex" message="A genome version name is required">\S+</validator>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="snpeffdbv40" name="snpeff_db" label="${tool.name} ${genome_version}" />
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20 </outputs>
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21 <expand macro="stdio" />
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22 <help>
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24 @EXTERNAL_DOCUMENTATION@
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26 @CITATION_SECTION@
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28 </help>
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29 <expand macro="citations" />
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30 </tool>
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