Mercurial > repos > iuc > data_manager_snpeff
diff 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 |
---|---|
date | Mon, 31 Oct 2016 08:13:11 -0400 |
parents | 85a23e2dd92b |
children | 847b0f43c0e5 |
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--- a/data_manager/data_manager_snpEff_databases.xml Tue Jun 07 15:44:15 2016 -0400 +++ b/data_manager/data_manager_snpEff_databases.xml Mon Oct 31 08:13:11 2016 -0400 @@ -1,20 +1,23 @@ -<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data"> - <description>Read the list of available snpEff databases</description> - <requirements> - <requirement type="package" version="4.1">snpEff</requirement> - </requirements> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <command interpreter="python"> - data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file" - </command> - <inputs> - </inputs> - <outputs> +<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data"> + <description>Read the list of available snpEff databases</description> + <macros> + <import>snpEff_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command><![CDATA[ + @CONDA_SNPEFF_JAR_PATH@ && + python '$__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> + </outputs> <tests> <test> <output name="out_file"> @@ -25,7 +28,7 @@ </output> </test> </tests> - <help> + <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, @@ -36,9 +39,7 @@ 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> - <citations> - <citation type="doi">10.4161/fly.19695</citation> - </citations> + </help> + <expand macro="citations" /> </tool>