Mercurial > repos > iuc > snpeff
view snpEff_download.xml @ 29:ca2b512e8d7c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4cc10cfe702828a91ecf8bb58d3f84a36b0578f7
author | iuc |
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date | Mon, 21 Oct 2024 13:56:15 +0000 |
parents | 65ae79bddc69 |
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<tool id="snpEff_download" name="SnpEff download:" version="@SNPEFF_VERSION@+galaxy@WRAPPER_VERSION@" profile="23.0"> <description> download a pre-built database</description> <macros> <import>snpEff_macros.xml</import> </macros> <requirements> <expand macro="requirement" /> </requirements> <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ snpEff download -dataDir "\$PWD/temp" -v '$genome_version' && mkdir -p '$snpeff_db.files_path' && mv temp/'$genome_version' '$snpeff_db.files_path' ]]></command> <inputs> <param name="genome_version" type="text" value="" label="Select the annotation database you want to download (e.g. GRCh38.86, mm10 etc.)" help="The list of available databases can be obtained with 'SnpEff databases' tool"> <validator type="empty_field" message="A genome version name is required" /> </param> </inputs> <outputs> <data name="snpeff_db" format="snpeffdb" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}"/> </outputs> <tests> <test> <param name="genome_version" value="ebola_zaire"/> <output name="snpeff_db"> <assert_contents> <has_text text="ebola_zaire" /> </assert_contents> </output> </test> <test> <param name="genome_version" value="Bdellovibrio_bacteriovorus_hd100"/> <output name="snpeff_db"> <assert_contents> <has_text text="Bdellovibrio_bacteriovorus_hd100" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** This tool downloads a specified database from a remote SnpEff repository. It deposits it into the history. ------- .. class:: infomark **The usage scenario** Suppose you want to annoate a VCF file containing variants within mm10 version of the Mouse genome. To do this you can: #. Download mm10 snpEff database by typing *mm10* into **Select the annotation database...** text box. #. Use **SnpEff eff** by choosing the downloaded database from the history using *Downloaded snpEff database in your history* option of the **Genome source** parameter. @SNPEFF_IN_GALAXY_INFO@ @EXTERNAL_DOCUMENTATION@ ]]></help> <expand macro="citations" /> </tool>