Mercurial > repos > iuc > snpsift
view snpSift_vartype.xml @ 1:98708b88af9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author | iuc |
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date | Tue, 07 Jun 2016 10:04:09 -0400 |
parents | 9e8280e19338 |
children | bf8c1526871b |
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<tool id="snpsift_vartype" name="SnpSift Variant Type" version="@WRAPPER_VERSION@.0"> <description>Annotate with variant type</description> <macros> <import>snpSift_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ 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> <tests> </tests> <help><![CDATA[ **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>