|
0
|
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> $log > $output
|
|
|
9 </command>
|
|
|
10 <inputs>
|
|
|
11 <param format="vcf" name="input" type="data" label="Variant file (VCF)"/>
|
|
|
12 </inputs>
|
|
|
13 <outputs>
|
|
|
14 <data format="vcf" name="output" label="${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>
|
