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2
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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.3" tool_type="manage_data">
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0
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2 <description>Download a new database</description>
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3 <requirements>
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2
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4 <requirement type="package" version="3.3">snpEff</requirement>
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0
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5 </requirements>
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6 <command interpreter="python">
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2
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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 "${genome_databases.fields.value}"
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9 --organism "${genome_databases.fields.name}"
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10 "$out_file"
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11 </command>
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12 <inputs>
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13 <param name="genome_databases" type="select" label="Genome Version">
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14 <options from_data_table="snpeff_databases"/>
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15 </param>
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16 </inputs>
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17
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18 <outputs>
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19 <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome_databases.fields.value}"/>
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20 </outputs>
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21 <stdio>
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22 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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23 <exit_code range="1:" level="fatal" description="Error" />
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24 </stdio>
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4
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25 <tests>
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26 <test>
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27 <param name="genome_databases" value="GRCh37.71"/>
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28 <output name="out_file">
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29 <assert_contents>
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30 <!-- Check that a genome was added -->
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31 <has_text text="GRCh37.71" />
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32 <has_text text="snpeff_regulationdb" />
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33 <has_text text="snpeff_annotations" />
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34 </assert_contents>
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35 </output>
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36 </test>
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37 </tests>
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0
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38 <help>
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39
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40 This tool downloads a SnpEff database.
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41
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42 For details about this tool, please go to http://snpEff.sourceforge.net
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43
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44 </help>
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45 </tool>
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46
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