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1 <tool id="snpEff" name="SnpEff" version="2.5">
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2 <description>predicts SNP effect from a genomic VCF file</description>
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3 <requirements>
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4 <requirement type="package" version="4.0">snpEff</requirement>
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5 </requirements>
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6
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7 <!--
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8 You will need to change the path to wherever your installation is.
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9 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
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10 -->
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11 <command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command>
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12 <inputs>
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13 <param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/>
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14 <param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/>
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15 <param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/>
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16
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17 </inputs>
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18 <outputs>
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19 <data format="vcf" name="output" label="Annotated VCF" />
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20 <data format="html" name="statsFile" label="HTML statistics output"/>
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21 <data format="txt" name="log" label="Log file"/>
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22 </outputs>
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23
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24 <help>
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25
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26
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27
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28
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29
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30 .. class:: infomark
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31
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32 **Program encapsulated in Galaxy by Southgreen**
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33
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34 .. class:: infomark
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35
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36 **SnpEff version 2.5**
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37
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38 -----
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39
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40 ==============
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41 Please cite:
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42 ==============
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43
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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.
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45
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46 -----
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47
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48 ===========
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49 Overview:
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50 ===========
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51
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52 Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
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53
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54 -----
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55
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56 For further informations, please visite the SnpEff_ website.
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57
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58
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59 .. _SnpEff: http://snpeff.sourceforge.net/
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60 </help>
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61
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62 </tool>
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63
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