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1 <tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="3.6" tool_type="manage_data">
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2 <description>Read the list of available snpEff databases</description>
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3 <requirements>
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4 <requirement type="package" version="3.6">snpEff</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 data_manager_snpEff_databases.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar "$out_file"
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8 </command>
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9 <inputs>
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10 </inputs>
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11 <outputs>
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12 <data name="out_file" format="data_manager_json"/>
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13 </outputs>
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14 <stdio>
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15 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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16 <exit_code range="1:" level="fatal" description="Error" />
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17 </stdio>
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18 <tests>
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19 <test>
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20 <output name="out_file">
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21 <assert_contents>
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22 <!-- Check that a genome was added -->
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23 <has_text text="GRCh37.72" />
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24 </assert_contents>
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25 </output>
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26 </test>
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27 </tests>
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28 <help>
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29
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30 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
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31 It should only need to be run once for a snpEff version,
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32 since it populates the SnpEff Download data manager from the snpEff config file.
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33
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34 For information about snpEff: http://snpEff.sourceforge.net
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35
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36 Please cite:
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37 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
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38
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39 </help>
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40 </tool>
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41
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