Mercurial > repos > iuc > snpsift
diff snpSift_vartype.xml @ 0:9e8280e19338 draft
Uploaded
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpSift_vartype.xml Thu Jan 22 08:39:07 2015 -0500 @@ -0,0 +1,39 @@ +<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>