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| author | dereeper |
|---|---|
| date | Fri, 20 Apr 2018 09:04:25 -0400 |
| parents | c6640c49fd01 |
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<tool id="annotationStatsFromVCF" name="Get VCF annotation statistics" version="2.0.0"> <description>Get annotation fromi a VCF file annotated by snpeff</description> <requirements> <requirement type="binary">perl</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> <requirement type="package" version="0.1.14">vcftools</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="perl"> AnnotationStatsFromVCF.pl -v $input -o $output_label -s $step && mv ${output_label} $output_count && mv ${output_label}.effect $output_stats_effect && mv ${output_label}.location $output_stats_location </command> <inputs> <param type="data" name="input" format="vcf" label="VCF file" /> <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> <param type="text" name="output_label" label="Output_label" value='VCF_stats' optional='false' /> </inputs> <outputs> <data name="output_count" format="txt" label="${output_label}"/> <data name="output_stats_effect" format="txt" label="${output_label}.effect"/> <data name="output_stats_location" format="txt" label="${output_label}.location"/> </outputs> <tests> <test> <param name="input" value="annotationStatsFromVCF.vcf"/> <param name="step" value="50000"/> <output name="output_count" file="annotationStatsFromVCF.txt"/> <output name="output_stats_effect" file="annotationStatsFromVCF.effect"/> <output name="output_stats_location" file="annotationStatsFromVCF.location"/> </test> </tests> <help><![CDATA[ .. class:: infomark **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | **Please cite** "SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations", **Dereeper A. et al.**, Nucl. Acids Res. (1 july 2015) 43 (W1). .. class:: infomark **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- ========================= Get annotation statistics ========================= ----------- Description ----------- | Get annotation statistics from VCF ------------ Dependencies ------------ VCFtools vcftools_ 0.1.14, Conda version Bioperl perl-bioperl_ 1.6.924, Conda version .. _vcftools: https://anaconda.org/bioconda/vcftools .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl ---------- Input file ---------- VCF file VCF file ---------- Parameters ---------- Step Step in bp Output label Prefix for the ouput files ------------ Output files ------------ Output_name Output_name.effect file Output_name.location file --------------------------------------------------- --------------- Working example --------------- Input file ========== VCF file --------- :: #fileformat=VCFv4.1 #FILTER=<ID=LowQual,Description="Low quality"> #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> [...] CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 Parameters ========== Step -> 50000 Output label -> VCF_stats Output files ============ VCF_stats ---------------------------------- :: Chrom Bin dN/dS ratio chr1 50000 0.791666666666667 chr1 100000 0.981132075471698 chr1 150000 2.08333333333333 VCF_stats.effect -------------------- :: Intron 960 Intron:960 UTR 281 UTR:281 Exon 3248 Synonym:124 Non-syn:120 VCF_stats.location -------------------- :: Intergenic 466 Intergenic:466 Genic 4489 Exon:3248 Intron:960 UTR:281 ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry --> <citation type="bibtex">@article{Dereeper03062015, author = {Dereeper, Alexis and Homa, Felix and Andres, Gwendoline and Sempere, Guilhem and Sarah, Gautier and Hueber, Yann and Dufayard, Jean-François and Ruiz, Manuel}, title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, year = {2015}, doi = {10.1093/nar/gkv351}, abstract ={SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density. Additionally, we developed a suite of Galaxy wrappers for each step of the SNiPlay3 process, so that the complete pipeline can also be deployed on a Galaxy instance using the Galaxy ToolShed procedure and then be computed as a Galaxy workflow. SNiPlay is accessible at http://sniplay.southgreen.fr.}, URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, journal = {Nucleic Acids Research} } }</citation> </citations> </tool>