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author dereeper
date Mon, 16 Apr 2018 08:56:29 -0400
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1 <tool id="snpEff" name="SnpEff" version="2.0.0">
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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="4.3.1">snpEff</requirement>
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5 </requirements>
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7 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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8 <stdio>
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9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12
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13 <!--
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14 You will need to change the path to wherever your installation is.
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15 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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16 -->
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17 <command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command>
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18 <inputs>
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19 <param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/>
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20 <param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/>
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21 <param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/>
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22
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23 </inputs>
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24 <outputs>
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25 <data format="vcf" name="output" label="Annotated VCF" />
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26 <data format="html" name="statsFile" label="HTML statistics output"/>
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27 <data format="txt" name="log" label="Log file"/>
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28 </outputs>
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29
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30 <tests>
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31 <test>
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32 <param name="vcf" value="snpeff_input.vcf"/>
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33 <param name="genome" value="snpeff_in.fasta"/>
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34 <param name="gff" value="snpeff_in.gff3"/>
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35 <output name="output" file="snpeff_output.vcf" compare="diff" lines_diff="4"/>
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36 </test>
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37 </tests>
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38
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39 <help><![CDATA[
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40
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41 .. class:: infomark
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42
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43 **SnpEff** version 4.0
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44 | **Please cite** "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 .. class:: infomark
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47
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48 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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49
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50 .. class:: infomark
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52 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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54 ---------------------------------------------------
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56 ======
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57 SnpEff
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58 ======
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60 -----------
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61 Description
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62 -----------
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63
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64 | 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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65 | For further informations, please visit the SnpEff website_.
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66
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67 .. _website: http://snpeff.sourceforge.net/
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68
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69 ------------
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70 Dependencies
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71 ------------
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72 SnpEff
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73 SnpEff_ 4.3.1, Conda version
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75 .. _snpeff: https://anaconda.org/bioconda/snpeff
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77 ]]></help>
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78 <citations>
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79 <citation type="doi">10.4161/fly.19695</citation>
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80 </citations>
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81 </tool>
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