Mercurial > repos > dereeper > snpeff_from_gff_vcf
diff snpEff.xml @ 1:633d264f8888 draft default tip
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
|---|---|
| date | Mon, 16 Apr 2018 08:56:29 -0400 |
| parents | abde5b0387c8 |
| children |
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--- a/snpEff.xml Mon Mar 23 05:17:19 2015 -0400 +++ b/snpEff.xml Mon Apr 16 08:56:29 2018 -0400 @@ -1,9 +1,15 @@ -<tool id="snpEff" name="SnpEff" version="4.0"> - <description>predicts SNP effect from a genomic VCF file</description> +<tool id="snpEff" name="SnpEff" version="2.0.0"> + <description>Predicts SNP effect from a genomic VCF file</description> <requirements> - <requirement type="package" version="4.0">snpEff</requirement> + <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) @@ -21,43 +27,56 @@ <data format="txt" name="log" label="Log file"/> </outputs> - <help> - + <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 -**Program encapsulated in Galaxy by Southgreen** +**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 -**SnpEff version 4.0** +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr ------ +--------------------------------------------------- -============== - Please cite: -============== +====== +SnpEff +====== -"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. +----------- +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_. -=========== - Overview: -=========== - -Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). +.. _website: http://snpeff.sourceforge.net/ ------ - -For further informations, please visite the SnpEff_ website. +------------ +Dependencies +------------ +SnpEff + SnpEff_ 4.3.1, Conda version +.. _snpeff: https://anaconda.org/bioconda/snpeff -.. _SnpEff: http://snpeff.sourceforge.net/ - </help> - + ]]></help> + <citations> + <citation type="doi">10.4161/fly.19695</citation> + </citations> </tool>