<tool id="snpEff" name="SnpEff" version="2.0.0">
	<description>Predicts SNP effect from a genomic VCF file</description>
	<requirements>
		<requirement type="package" version="4.3.1">snpEff</requirement>
	</requirements> 	

        <!-- [STRONGLY RECOMMANDED] Exit code rules -->
        <stdio>
            <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
            <exit_code range="1:" level="fatal" />
        </stdio>

	<!-- 
	    You will need to change the path to wherever your installation is.
		You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
	-->
	<command interpreter="bash">./snpEff-pipe.sh $vcf $genome $gff $output $statsFile $log</command>
	<inputs>
		<param format="vcf" name="vcf" type="data" label="VCF input file" help="Positions must be genomic positions"/>
		<param format="fasta" name="genome" type="data" label="Reference genome in Fasta" help=""/>
		<param format="gff3" name="gff" type="data" label="GFF annotation of the genome" help=""/>

	</inputs>
	<outputs>
		<data format="vcf" name="output" label="Annotated VCF" />
		<data format="html" name="statsFile" label="HTML statistics output"/>
		<data format="txt" name="log" label="Log file"/>
	</outputs>

    <tests>
        <test>
            <param name="vcf" value="snpeff_input.vcf"/>
            <param name="genome" value="snpeff_in.fasta"/>
            <param name="gff" value="snpeff_in.gff3"/>
            <output name="output" file="snpeff_output.vcf" compare="diff" lines_diff="4"/>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

**SnpEff** version 4.0
  | **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.

.. class:: infomark

**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

---------------------------------------------------

======
SnpEff
======

-----------
Description
-----------

  | Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
  | For further informations, please visit the SnpEff website_.

.. _website: http://snpeff.sourceforge.net/

------------
Dependencies
------------
SnpEff
        SnpEff_ 4.3.1, Conda version

.. _snpeff: https://anaconda.org/bioconda/snpeff

    ]]></help>
    <citations>
       <citation type="doi">10.4161/fly.19695</citation>
    </citations>
</tool>