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annotate snpEff_download.xml @ 22:4430626bd994

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Use snpeffect_genomedb.loc for genomeVersions, have snpEff attempt to download genomeVersions that are not already locally cached
author Jim Johnson <jj@umn.edu>
date Thu, 17 Jan 2013 13:00:52 -0600
parents 1cae7fb31da7
children 50c1a8ff6c82
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1 <tool id="snpEff_download" name="SnpEff Download" version="1.0">
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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="3.1">snpEff</requirement>
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5 </requirements>
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6 <command>java -jar \$JAVA_JAR_PATH/snpEff.jar download -c \$JAVA_JAR_PATH/snpEff.config $genomeVersion > $logfile </command>
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7 <inputs>
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8 <param name="genomeVersion" type="select" label="Genome">
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9 <options from_file="snpeffect_genomedb.loc">
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10 <column name="name" index="1"/>
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11 <column name="value" index="0"/>
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12 </options>
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13 </param>
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14 </inputs>
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16 <outputs>
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17 <data format="txt" name="logfile" />
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18 </outputs>
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19 <stdio>
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20 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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21 <exit_code range="1:" level="fatal" description="Error" />
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22 </stdio>
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24 <help>
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25
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26 This tool downloads a SnpEff database.
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28 For details about this tool, please go to http://snpEff.sourceforge.net
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30 </help>
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31 </tool>
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