Mercurial > repos > iuc > snpsift

comparison snpSift_vartype.xml @ 0:9e8280e19338 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Thu, 22 Jan 2015 08:39:07 -0500
parents
children 98708b88af9f
comparison
equal deleted inserted replaced
-1:000000000000 0:9e8280e19338
1 <tool id="snpsift_vartype" name="SnpSift Variant Type" version="4.0.0">
2 <description>Annotate with variant type</description>
3 <expand macro="requirements" />
4 <macros>
5 <import>snpSift_macros.xml</import>
6 </macros>
7 <command>
8 java -jar \$SNPEFF_JAR_PATH/SnpSift.jar varType $input 2&gt; $log &gt; $output
9 </command>
10 <inputs>
11 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
12 </inputs>
13 <outputs>
14 <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
15 <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
16 </outputs>
17 <expand macro="stdio" />
18 <tests>
19 </tests>
20 <help>
21 **What it does**
22
23 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).
24
25 .. _SnpSift Variant type: http://snpeff.sourceforge.net/SnpSift.html#VariantType
26
27 ------
28
29 **License**
30
31 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
32
33 .. _CRS4 Srl.: http://www.crs4.it/
34 .. _MIT license: http://opensource.org/licenses/MIT
35
36 @CITATION_SECTION@
37 </help>
38 <expand macro="citations" />
39 </tool>