view data_manager/data_manager_vep_cache_download.xml @ 8:3f3246b8972e draft default tip

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<tool id="data_manager_vep_cache_download" name="Download and install VEP cache" version="0.1" tool_type="manage_data">
	<description>versioned annotation files for VEP</description>
	<macros>
		<token name="@VERSION@">105</token>
	</macros>
	<requirements>
		<requirement type="package" version="@VERSION@.0">ensembl-vep</requirement>
		<requirement type="package" version="3.6">python</requirement>
	</requirements>
	<command detect_errors="exit_code"><![CDATA[
		python '$__tool_directory__/data_manager_vep_cache_download.py' '$out_file' &&
		vep_convert_cache -r -d '${out_file.extra_files_path}' -s all -v all
	]]></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-@VERSION@/variation/indexed_vep_cache/"
			label="FTP root url for VEP cache files" help="Release number should be equal to desired VEP version"/>
		<param name="file_name" type="text" label="File name of cache file to be downloaded from root url" help="E.g. homo_sapiens_vep_@VERSION@_GRCh38.tar.gz"/>
	</inputs>
	<outputs>
		<data name="out_file" format="data_manager_json"/>
	</outputs>
	<tests>
	<test>
		<param name="dbkey" value="ci3"/>
		<param name="url" value="http://ftp.ensembl.org/pub/release-@VERSION@/variation/indexed_vep_cache/"/>
		<param name="file_name" value="ciona_intestinalis_refseq_vep_@VERSION@_KH.tar.gz"/>
		<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_annotation_cache" 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>