sniplay: AnnotationStatsFromVCF/annotationStatsFromVCF

annotate AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml @ 11:15b23cdde685 draft

planemo upload commit 305985afd3b7c3d47f531149c2f1a279af2d12aa-dirty

author	dereeper
date	Fri, 20 Apr 2018 09:04:25 -0400
parents	c6640c49fd01
children

rev	line source
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	1 <tool id="annotationStatsFromVCF" name="Get VCF annotation statistics" version="2.0.0">
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	2 <description>Get annotation fromi a VCF file annotated by snpeff</description>
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	3 <requirements>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	4 <requirement type="binary">perl</requirement>
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	6 <requirement type="package" version="0.1.14">vcftools</requirement>
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	7 </requirements>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	8 <stdio>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	9 <exit_code range="1:" />
98c37a5d67f4 Uploaded dereeper parents: diff changeset	10 </stdio>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	11 <command interpreter="perl">
98c37a5d67f4 Uploaded dereeper parents: diff changeset	12 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 $output_stats_location
98c37a5d67f4 Uploaded dereeper parents: diff changeset	13 </command>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	14 <inputs>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	15 <param type="data" name="input" format="vcf" label="VCF file" />
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	16 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	17 <param type="text" name="output_label" label="Output_label" value='VCF_stats' optional='false' />
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	18 </inputs>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	19 <outputs>
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	20 <data name="output_count" format="txt" label="${output_label}"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	21 <data name="output_stats_effect" format="txt" label="${output_label}.effect"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	22 <data name="output_stats_location" format="txt" label="${output_label}.location"/>
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	23 </outputs>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	24 <tests>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	25 <test>
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	26 <param name="input" value="annotationStatsFromVCF.vcf"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	27 <param name="step" value="50000"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	28 <output name="output_count" file="annotationStatsFromVCF.txt"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	29 <output name="output_stats_effect" file="annotationStatsFromVCF.effect"/>
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	30 <output name="output_stats_location" file="annotationStatsFromVCF.location"/>
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	31 </test>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	32 </tests>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	33 <help><![CDATA[
98c37a5d67f4 Uploaded dereeper parents: diff changeset	34
98c37a5d67f4 Uploaded dereeper parents: diff changeset	35 .. class:: infomark
98c37a5d67f4 Uploaded dereeper parents: diff changeset	36
98c37a5d67f4 Uploaded dereeper parents: diff changeset	37 Authors Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
98c37a5d67f4 Uploaded dereeper parents: diff changeset	38
98c37a5d67f4 Uploaded dereeper parents: diff changeset	39 \| 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).
98c37a5d67f4 Uploaded dereeper parents: diff changeset	40
98c37a5d67f4 Uploaded dereeper parents: diff changeset	41 .. class:: infomark
98c37a5d67f4 Uploaded dereeper parents: diff changeset	42
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	43 Galaxy integration Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	44
98c37a5d67f4 Uploaded dereeper parents: diff changeset	45 .. class:: infomark
98c37a5d67f4 Uploaded dereeper parents: diff changeset	46
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	47 Support For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	48
98c37a5d67f4 Uploaded dereeper parents: diff changeset	49 ---------------------------------------------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	50
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	51 =========================
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	52 Get annotation statistics
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	53 =========================
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	54
98c37a5d67f4 Uploaded dereeper parents: diff changeset	55 -----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	56 Description
98c37a5d67f4 Uploaded dereeper parents: diff changeset	57 -----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	58
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	59 \| Get annotation statistics from VCF
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	60
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	61 ------------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	62 Dependencies
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	63 ------------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	64 VCFtools
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	65 vcftools_ 0.1.14, Conda version
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	66 Bioperl
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	67 perl-bioperl_ 1.6.924, Conda version
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	68
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	69 .. _vcftools: https://anaconda.org/bioconda/vcftools
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	70 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	71
98c37a5d67f4 Uploaded dereeper parents: diff changeset	72 ----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	73 Input file
98c37a5d67f4 Uploaded dereeper parents: diff changeset	74 ----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	75
98c37a5d67f4 Uploaded dereeper parents: diff changeset	76 VCF file
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	77 VCF file
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	78
98c37a5d67f4 Uploaded dereeper parents: diff changeset	79 ----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	80 Parameters
98c37a5d67f4 Uploaded dereeper parents: diff changeset	81 ----------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	82
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	83 Step
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	84 Step in bp
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	85
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	86 Output label
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	87 Prefix for the ouput files
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	88
98c37a5d67f4 Uploaded dereeper parents: diff changeset	89 ------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	90 Output files
98c37a5d67f4 Uploaded dereeper parents: diff changeset	91 ------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	92
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	93 Output_name
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	94
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	95 Output_name.effect file
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	96
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	97 Output_name.location file
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	98
98c37a5d67f4 Uploaded dereeper parents: diff changeset	99 ---------------------------------------------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	100
98c37a5d67f4 Uploaded dereeper parents: diff changeset	101 ---------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	102 Working example
98c37a5d67f4 Uploaded dereeper parents: diff changeset	103 ---------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	104
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	105 Input file
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	106 ==========
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	107
98c37a5d67f4 Uploaded dereeper parents: diff changeset	108 VCF file
98c37a5d67f4 Uploaded dereeper parents: diff changeset	109 ---------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	110
98c37a5d67f4 Uploaded dereeper parents: diff changeset	111 ::
98c37a5d67f4 Uploaded dereeper parents: diff changeset	112
98c37a5d67f4 Uploaded dereeper parents: diff changeset	113 #fileformat=VCFv4.1
98c37a5d67f4 Uploaded dereeper parents: diff changeset	114 #FILTER=<ID=LowQual,Description="Low quality">
98c37a5d67f4 Uploaded dereeper parents: diff changeset	115 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
98c37a5d67f4 Uploaded dereeper parents: diff changeset	116 [...]
98c37a5d67f4 Uploaded dereeper parents: diff changeset	117 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA
98c37a5d67f4 Uploaded dereeper parents: diff changeset	118 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0\|0:0:1,0,0
98c37a5d67f4 Uploaded dereeper parents: diff changeset	119
98c37a5d67f4 Uploaded dereeper parents: diff changeset	120
98c37a5d67f4 Uploaded dereeper parents: diff changeset	121 Parameters
98c37a5d67f4 Uploaded dereeper parents: diff changeset	122 ==========
98c37a5d67f4 Uploaded dereeper parents: diff changeset	123
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	124 Step -> 50000
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	125 Output label -> VCF_stats
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	126
98c37a5d67f4 Uploaded dereeper parents: diff changeset	127
98c37a5d67f4 Uploaded dereeper parents: diff changeset	128 Output files
98c37a5d67f4 Uploaded dereeper parents: diff changeset	129 ============
98c37a5d67f4 Uploaded dereeper parents: diff changeset	130
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	131 VCF_stats
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	132 ----------------------------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	133
98c37a5d67f4 Uploaded dereeper parents: diff changeset	134 ::
98c37a5d67f4 Uploaded dereeper parents: diff changeset	135
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	136 Chrom Bin dN/dS ratio
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	137 chr1 50000 0.791666666666667
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	138 chr1 100000 0.981132075471698
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	139 chr1 150000 2.08333333333333
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	140
98c37a5d67f4 Uploaded dereeper parents: diff changeset	141
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	142 VCF_stats.effect
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	143 --------------------
98c37a5d67f4 Uploaded dereeper parents: diff changeset	144
98c37a5d67f4 Uploaded dereeper parents: diff changeset	145 ::
98c37a5d67f4 Uploaded dereeper parents: diff changeset	146
10 c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	147 Intron 960 Intron:960
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	148 UTR 281 UTR:281
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	149 Exon 3248 Synonym:124 Non-syn:120
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	150
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	151 VCF_stats.location
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	152 --------------------
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	153
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	154 ::
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	155
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	156 Intergenic 466 Intergenic:466
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	157 Genic 4489 Exon:3248 Intron:960 UTR:281
c6640c49fd01 planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac dereeper parents: 9 diff changeset	158
9 98c37a5d67f4 Uploaded dereeper parents: diff changeset	159
98c37a5d67f4 Uploaded dereeper parents: diff changeset	160 ]]></help>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	161 <citations>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	162 <!-- [HELP] As DOI or BibTex entry -->
98c37a5d67f4 Uploaded dereeper parents: diff changeset	163 <citation type="bibtex">@article{Dereeper03062015,
98c37a5d67f4 Uploaded dereeper parents: diff changeset	164 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},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	165 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	166 year = {2015},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	167 doi = {10.1093/nar/gkv351},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	168 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.},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	169 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	170 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
98c37a5d67f4 Uploaded dereeper parents: diff changeset	171 journal = {Nucleic Acids Research}
98c37a5d67f4 Uploaded dereeper parents: diff changeset	172 }
98c37a5d67f4 Uploaded dereeper parents: diff changeset	173
98c37a5d67f4 Uploaded dereeper parents: diff changeset	174 }</citation>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	175
98c37a5d67f4 Uploaded dereeper parents: diff changeset	176 </citations>
98c37a5d67f4 Uploaded dereeper parents: diff changeset	177
98c37a5d67f4 Uploaded dereeper parents: diff changeset	178 </tool>

Mercurial > repos > dereeper > sniplay

annotate AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml @ 11:15b23cdde685 draft