Mercurial > repos > iuc > snpeff

annotate snpEff_download.xml @ 6:20f0429a4bfe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit bd4fbe120288bf8452e479cbd82aa1bbf5c4bd31
author iuc
date Mon, 19 Dec 2016 11:56:53 -0500
parents 698ef30638a8
children 7adfd0589f49
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1 <tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
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2 <description>Download a new database</description>
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3 <macros>
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4 <import>snpEff_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 @CONDA_SNPEFF_JAR_PATH@ &&
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12 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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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
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17 <help>@SNPEFF_DATABASE_URL@</help>
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18 <validator type="regex" message="A genome version name is required">\S+</validator>
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19 </param>
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20 </inputs>
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21 <outputs>
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22 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="genome_version" value="ebola_zaire"/>
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27 <output name="snpeff_db">
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28 <assert_contents>
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29 <has_text text="ebola_zaire" />
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30 </assert_contents>
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31 </output>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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36 @EXTERNAL_DOCUMENTATION@
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38 ]]>
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39 </help>
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40 <expand macro="citations" />
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41 </tool>
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