view data_manager/data_manager_vep_cache_download.xml @ 2:612026ea6db5 draft

Uploaded first real version

<tool id="data_manager_vep_cache_downloader" name="Download and install VEP cache" version="0.1" tool_type="manage_data">
    <description>the cache files required by VEP</description>
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
    </requirements>
    <command detect_errors="exit_code">
        python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file'
    </command>
    <inputs>
        <param name="dbkey" type="genomebuild"
			label="DBKEY of genome that the VEP cache data is for"
			help="" />
        <param name="url" type="text" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"
            label="FTP root url for VEP cache files" help=""/>
		<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"/>
		<param name="display_name" type="text" label="Display name used in data-selection dropdowns." help="E.g. Homo sapiens hg38 (V105)"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
		<test>
            <param name="dbkey" value="ce11"/>
            <param name="url" value="http://ftp.ensembl.org/pub/release-105/variation/indexed_vep_cache/"/>
			<param name="file_name" value="caenorhabditis_elegans_vep_105_WBcel235.tar.gz"/>
			<param name="display_name" value="C. elegans c11 (V105)"/>
            <output name="out_file" file="from_test-meta.data_manager.json"/>
        </test>
    </tests>
    <help>
This tool downloads given versions of VEP cache annotation files and makes them available to Ensembl VEP in Galaxy via the
"vep_versioned_caches" data table. You should use the indexed version of the cache files and it is strongly recommended to 
use the cache files which version number matches the VEP version number. Note that for most genomes there are three versions 
of cache data available: default, refseq and merged (combining the former two). Choose the one suitable for your usage. 

A general introduction to the VEP cache and download links can be found on the official website:
https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
    </help>
    <citations>
        <citation type="doi">10.1186/s13059-016-0974-4</citation>
    </citations>
</tool>