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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0.0" 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="4.0">snpEff</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config
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8 --genome_version "$genome_version" "$out_file"
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9 </command>
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10 <inputs>
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11 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
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12 <help>https://snpeff-data.galaxyproject.org/databases/</help>
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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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16
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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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19 </outputs>
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20 <stdio>
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21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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22 <exit_code range="1:" level="fatal" description="Error" />
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23 </stdio>
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24 <tests>
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25 <test>
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26 <param name="genome_version" value="GRCh38.76"/>
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27 <output name="out_file">
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28 <assert_contents>
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29 <!-- Check that a genome was added -->
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30 <has_text text="GRCh38.76" />
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31 <has_text text="snpeffv_regulationdb" />
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32 <has_text text="snpeffv_annotations" />
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33 </assert_contents>
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34 </output>
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35 </test>
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36 </tests>
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37 <help>
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38
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39 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations.
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40
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41 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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42
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43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/
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44
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45
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46 For details about this tool, please go to http://snpEff.sourceforge.net
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47
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48 Please cite:
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49 "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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50
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51 </help>
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52 </tool>
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53
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