Mercurial > repos > dereeper > snpeff_from_gff_vcf
comparison snpEff.xml @ 0:abde5b0387c8 draft
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| author | dereeper |
|---|---|
| date | Mon, 23 Mar 2015 05:17:19 -0400 |
| parents | |
| children | 633d264f8888 |
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| -1:000000000000 | 0:abde5b0387c8 |
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| 1 <tool id="snpEff" name="SnpEff" version="4.0"> | |
| 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 4.0** | |
| 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 |