Mercurial > repos > iuc > snpsift
comparison snpSift_vartype.xml @ 0:9e8280e19338 draft
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> $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> |