Mercurial > repos > dereeper > snpeff_from_gff_vcf
comparison 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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| 0:abde5b0387c8 | 1:633d264f8888 |
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| 1 <tool id="snpEff" name="SnpEff" version="4.0"> | 1 <tool id="snpEff" name="SnpEff" version="2.0.0"> |
| 2 <description>predicts SNP effect from a genomic VCF file</description> | 2 <description>Predicts SNP effect from a genomic VCF file</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="4.0">snpEff</requirement> | 4 <requirement type="package" version="4.3.1">snpEff</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 | |
| 7 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 8 <stdio> | |
| 9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 10 <exit_code range="1:" level="fatal" /> | |
| 11 </stdio> | |
| 6 | 12 |
| 7 <!-- | 13 <!-- |
| 8 You will need to change the path to wherever your installation is. | 14 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) | 15 You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
| 10 --> | 16 --> |
| 19 <data format="vcf" name="output" label="Annotated VCF" /> | 25 <data format="vcf" name="output" label="Annotated VCF" /> |
| 20 <data format="html" name="statsFile" label="HTML statistics output"/> | 26 <data format="html" name="statsFile" label="HTML statistics output"/> |
| 21 <data format="txt" name="log" label="Log file"/> | 27 <data format="txt" name="log" label="Log file"/> |
| 22 </outputs> | 28 </outputs> |
| 23 | 29 |
| 24 <help> | 30 <tests> |
| 31 <test> | |
| 32 <param name="vcf" value="snpeff_input.vcf"/> | |
| 33 <param name="genome" value="snpeff_in.fasta"/> | |
| 34 <param name="gff" value="snpeff_in.gff3"/> | |
| 35 <output name="output" file="snpeff_output.vcf" compare="diff" lines_diff="4"/> | |
| 36 </test> | |
| 37 </tests> | |
| 25 | 38 |
| 26 | 39 <help><![CDATA[ |
| 27 | |
| 28 | |
| 29 | 40 |
| 30 .. class:: infomark | 41 .. class:: infomark |
| 31 | 42 |
| 32 **Program encapsulated in Galaxy by Southgreen** | 43 **SnpEff** version 4.0 |
| 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. | |
| 33 | 45 |
| 34 .. class:: infomark | 46 .. class:: infomark |
| 35 | 47 |
| 36 **SnpEff version 4.0** | 48 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) |
| 37 | 49 |
| 38 ----- | 50 .. class:: infomark |
| 39 | 51 |
| 40 ============== | 52 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 41 Please cite: | |
| 42 ============== | |
| 43 | 53 |
| 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. | 54 --------------------------------------------------- |
| 45 | 55 |
| 46 ----- | 56 ====== |
| 57 SnpEff | |
| 58 ====== | |
| 47 | 59 |
| 48 =========== | 60 ----------- |
| 49 Overview: | 61 Description |
| 50 =========== | 62 ----------- |
| 51 | 63 |
| 52 Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). | 64 | Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). |
| 65 | For further informations, please visit the SnpEff website_. | |
| 53 | 66 |
| 54 ----- | 67 .. _website: http://snpeff.sourceforge.net/ |
| 55 | 68 |
| 56 For further informations, please visite the SnpEff_ website. | 69 ------------ |
| 70 Dependencies | |
| 71 ------------ | |
| 72 SnpEff | |
| 73 SnpEff_ 4.3.1, Conda version | |
| 57 | 74 |
| 75 .. _snpeff: https://anaconda.org/bioconda/snpeff | |
| 58 | 76 |
| 59 .. _SnpEff: http://snpeff.sourceforge.net/ | 77 ]]></help> |
| 60 </help> | 78 <citations> |
| 61 | 79 <citation type="doi">10.4161/fly.19695</citation> |
| 80 </citations> | |
| 62 </tool> | 81 </tool> |
| 63 | 82 |