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annotate snpEff_download.xml @ 23:924af057bbca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
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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 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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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
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16 <help>@SNPEFF_DATABASE_URL@</help>
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17 <validator type="regex" message="A genome version name is required">\S+</validator>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="genome_version" value="ebola_zaire"/>
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26 <output name="snpeff_db">
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27 <assert_contents>
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28 <has_text text="ebola_zaire" />
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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35 @EXTERNAL_DOCUMENTATION@
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37 ]]>
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38 </help>
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39 <expand macro="citations" />
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40 </tool>
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