Mercurial > repos > dereeper > sniplay3
comparison snpEff/.svn/text-base/snpEff.xml.svn-base @ 20:13cff72ec2d3 draft
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author | dereeper |
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date | Mon, 23 Mar 2015 05:30:36 -0400 |
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1 <tool id="snpEff" name="SnpEff" version="2.5"> | |
2 <description>predicts SNP effect from a genomic VCF file</description> | |
3 <requirements> | |
4 <requirement type="package" version="4.0">snpEff</requirement> | |
5 </requirements> | |
6 | |
7 <!-- | |
8 You will need to change the path to wherever your installation is. | |
9 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) | |
10 --> | |
11 <command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command> | |
12 <inputs> | |
13 <param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/> | |
14 <param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/> | |
15 <param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/> | |
16 | |
17 </inputs> | |
18 <outputs> | |
19 <data format="vcf" name="output" label="Annotated VCF" /> | |
20 <data format="html" name="statsFile" label="HTML statistics output"/> | |
21 <data format="txt" name="log" label="Log file"/> | |
22 </outputs> | |
23 | |
24 <help> | |
25 | |
26 | |
27 | |
28 | |
29 | |
30 .. class:: infomark | |
31 | |
32 **Program encapsulated in Galaxy by Southgreen** | |
33 | |
34 .. class:: infomark | |
35 | |
36 **SnpEff version 2.5** | |
37 | |
38 ----- | |
39 | |
40 ============== | |
41 Please cite: | |
42 ============== | |
43 | |
44 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", **Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.**, Fly (Austin). 2012 Apr-Jun;6(2):80-92. | |
45 | |
46 ----- | |
47 | |
48 =========== | |
49 Overview: | |
50 =========== | |
51 | |
52 Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). | |
53 | |
54 ----- | |
55 | |
56 For further informations, please visite the SnpEff_ website. | |
57 | |
58 | |
59 .. _SnpEff: http://snpeff.sourceforge.net/ | |
60 </help> | |
61 | |
62 </tool> | |
63 |