Mercurial > repos > iuc > data_manager_snpeff
view data_manager/data_manager_snpEff_databases.xml @ 3:e5a471c4630e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit de422632b9310905f8e9d44faee9ff768752968f
author | iuc |
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date | Mon, 31 Oct 2016 08:13:11 -0400 |
parents | 85a23e2dd92b |
children | 847b0f43c0e5 |
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<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data"> <description>Read the list of available snpEff databases</description> <macros> <import>snpEff_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ @CONDA_SNPEFF_JAR_PATH@ && python '$__tool_directory__/data_manager_snpEff_databases.py' --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar' '$out_file' ]]> </command> <inputs> </inputs> <outputs> <data name="out_file" format="data_manager_json"/> </outputs> <tests> <test> <output name="out_file"> <assert_contents> <!-- Check that a genome was added --> <has_text text="GRCh38.76" /> </assert_contents> </output> </test> </tests> <help> This tool updatess the list of SnpEff databases for the SnpEff Download data manager. It should only need to be run once for a snpEff version, since it populates the SnpEff Download data manager from the snpEff config file. For information about snpEff: http://snpEff.sourceforge.net Please cite: "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] </help> <expand macro="citations" /> </tool>