Mercurial > repos > iuc > snpsift
view snpSift_vartype.xml @ 0:9e8280e19338 draft
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author | iuc |
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date | Thu, 22 Jan 2015 08:39:07 -0500 |
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children | 98708b88af9f |
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<tool id="snpsift_vartype" name="SnpSift Variant Type" version="4.0.0"> <description>Annotate with variant type</description> <expand macro="requirements" /> <macros> <import>snpSift_macros.xml</import> </macros> <command> java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2> $log > $output </command> <inputs> <param format="vcf" name="input" type="data" label="Variant file (VCF)"/> </inputs> <outputs> <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" /> <data format="txt" name="log" label="${tool.name} on ${on_string}: log" /> </outputs> <expand macro="stdio" /> <tests> </tests> <help> **What it does** This tool uses `SnpSift Variant type`_ to add the variant type (SNP/MNP/INS/DEL/MIXED) in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense). .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType ------ **License** This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT @CITATION_SECTION@ </help> <expand macro="citations" /> </tool>