Mercurial > repos > dereeper > sniplay
annotate AnnotationStatsFromVCF/annotationStatsFromVCF_wrapper.xml @ 15:31c23d943c29 draft default tip
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| author | dereeper |
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| date | Tue, 08 Jan 2019 08:47:56 -0500 |
| parents | c6640c49fd01 |
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1 <tool id="annotationStatsFromVCF" name="Get VCF annotation statistics" version="2.0.0"> |
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2 <description>Get annotation fromi a VCF file annotated by snpeff</description> |
| 9 | 3 <requirements> |
| 4 <requirement type="binary">perl</requirement> | |
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5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
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6 <requirement type="package" version="0.1.14">vcftools</requirement> |
| 9 | 7 </requirements> |
| 8 <stdio> | |
| 9 <exit_code range="1:" /> | |
| 10 </stdio> | |
| 11 <command interpreter="perl"> | |
| 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 $output_stats_location | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param type="data" name="input" format="vcf" label="VCF file" /> | |
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16 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> |
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17 <param type="text" name="output_label" label="Output_label" value='VCF_stats' optional='false' /> |
| 9 | 18 </inputs> |
| 19 <outputs> | |
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20 <data name="output_count" format="txt" label="${output_label}"/> |
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21 <data name="output_stats_effect" format="txt" label="${output_label}.effect"/> |
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22 <data name="output_stats_location" format="txt" label="${output_label}.location"/> |
| 9 | 23 </outputs> |
| 24 <tests> | |
| 25 <test> | |
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26 <param name="input" value="annotationStatsFromVCF.vcf"/> |
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27 <param name="step" value="50000"/> |
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28 <output name="output_count" file="annotationStatsFromVCF.txt"/> |
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29 <output name="output_stats_effect" file="annotationStatsFromVCF.effect"/> |
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30 <output name="output_stats_location" file="annotationStatsFromVCF.location"/> |
| 9 | 31 </test> |
| 32 </tests> | |
| 33 <help><![CDATA[ | |
| 34 | |
| 35 .. class:: infomark | |
| 36 | |
| 37 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
| 38 | |
| 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). | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
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43 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 9 | 44 |
| 45 .. class:: infomark | |
| 46 | |
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47 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 48 |
| 49 --------------------------------------------------- | |
| 50 | |
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51 ========================= |
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52 Get annotation statistics |
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53 ========================= |
| 9 | 54 |
| 55 ----------- | |
| 56 Description | |
| 57 ----------- | |
| 58 | |
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59 | Get annotation statistics from VCF |
| 9 | 60 |
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61 ------------ |
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62 Dependencies |
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63 ------------ |
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64 VCFtools |
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65 vcftools_ 0.1.14, Conda version |
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66 Bioperl |
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67 perl-bioperl_ 1.6.924, Conda version |
| 9 | 68 |
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69 .. _vcftools: https://anaconda.org/bioconda/vcftools |
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70 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
| 9 | 71 |
| 72 ---------- | |
| 73 Input file | |
| 74 ---------- | |
| 75 | |
| 76 VCF file | |
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77 VCF file |
| 9 | 78 |
| 79 ---------- | |
| 80 Parameters | |
| 81 ---------- | |
| 82 | |
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83 Step |
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84 Step in bp |
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85 |
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86 Output label |
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87 Prefix for the ouput files |
| 9 | 88 |
| 89 ------------ | |
| 90 Output files | |
| 91 ------------ | |
| 92 | |
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93 Output_name |
| 9 | 94 |
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95 Output_name.effect file |
| 9 | 96 |
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97 Output_name.location file |
| 9 | 98 |
| 99 --------------------------------------------------- | |
| 100 | |
| 101 --------------- | |
| 102 Working example | |
| 103 --------------- | |
| 104 | |
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105 Input file |
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106 ========== |
| 9 | 107 |
| 108 VCF file | |
| 109 --------- | |
| 110 | |
| 111 :: | |
| 112 | |
| 113 #fileformat=VCFv4.1 | |
| 114 #FILTER=<ID=LowQual,Description="Low quality"> | |
| 115 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| 116 [...] | |
| 117 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA | |
| 118 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0 | |
| 119 | |
| 120 | |
| 121 Parameters | |
| 122 ========== | |
| 123 | |
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124 Step -> 50000 |
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125 Output label -> VCF_stats |
| 9 | 126 |
| 127 | |
| 128 Output files | |
| 129 ============ | |
| 130 | |
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131 VCF_stats |
| 9 | 132 ---------------------------------- |
| 133 | |
| 134 :: | |
| 135 | |
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136 Chrom Bin dN/dS ratio |
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137 chr1 50000 0.791666666666667 |
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138 chr1 100000 0.981132075471698 |
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139 chr1 150000 2.08333333333333 |
| 9 | 140 |
| 141 | |
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142 VCF_stats.effect |
| 9 | 143 -------------------- |
| 144 | |
| 145 :: | |
| 146 | |
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147 Intron 960 Intron:960 |
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148 UTR 281 UTR:281 |
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149 Exon 3248 Synonym:124 Non-syn:120 |
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150 |
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151 VCF_stats.location |
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152 -------------------- |
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153 |
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154 :: |
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155 |
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156 Intergenic 466 Intergenic:466 |
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157 Genic 4489 Exon:3248 Intron:960 UTR:281 |
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158 |
| 9 | 159 |
| 160 ]]></help> | |
| 161 <citations> | |
| 162 <!-- [HELP] As DOI or BibTex entry --> | |
| 163 <citation type="bibtex">@article{Dereeper03062015, | |
| 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}, | |
| 165 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 166 year = {2015}, | |
| 167 doi = {10.1093/nar/gkv351}, | |
| 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.}, | |
| 169 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 170 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 171 journal = {Nucleic Acids Research} | |
| 172 } | |
| 173 | |
| 174 }</citation> | |
| 175 | |
| 176 </citations> | |
| 177 | |
| 178 </tool> |