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1 <tool id="data_manager_vep_cache_download" name="Download and install VEP cache" version="0.1" tool_type="manage_data">
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2 <description>versioned annotation files for VEP</description>
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3 <requirements>
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4 <requirement type="package" version="3.9">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file'
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8 </command>
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9 <inputs>
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10 <param name="dbkey" type="genomebuild"
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11 label="DBKEY of genome that the VEP cache data is for"
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12 help="" />
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13 <param name="url" type="text" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"
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14 label="FTP root url for VEP cache files" help="Release number should be equal to desired VEP version"/>
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15 <param name="file_name" type="text" label="File name of cache file to be downloaded from root url" help="E.g. homo_sapiens_vep_105_GRCh38.tar.gz"/>
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16 </inputs>
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17 <outputs>
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18 <data name="out_file" format="data_manager_json"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="dbkey" value="ci3"/>
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23 <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/>
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24 <param name="file_name" value="ciona_intestinalis_refseq_vep_105_KH.tar.gz"/>
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25 <output name="out_file" file="from_test-meta.data_manager.json"/>
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26 </test>
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27 </tests>
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28 <help>
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29 This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the
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30 "vep_versioned_annotation_cache" data table. You should use the indexed version of the cache files and it is strongly
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31 recommended to use the cache files which version number matches the VEP version number. Note that for most genomes there
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32 are three versions of cache data available: default, refseq and merged (combining the former two). Choose the one suitable
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33 for your usage.
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34
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35 A general introduction to the VEP cache and download links can be found on the official website:
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36 https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
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37 </help>
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38 <citations>
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39 <citation type="doi">10.1186/s13059-016-0974-4</citation>
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40 </citations>
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41 </tool> |
