Mercurial > repos > dereeper > sniplay
annotate SNP_density/calculateSlidingWindowsSNPdensitiesFromVCF_wrapper.xml @ 14:d15869b3731a draft
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| author | dereeper |
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| date | Tue, 08 Jan 2019 08:46:57 -0500 |
| parents | c6640c49fd01 |
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| rev | line source |
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| 9 | 1 <tool id="sniplay_density" name="SNP density" version="2.0.0"> |
| 2 | |
| 3 <!-- [REQUIRED] Tool description displayed after the tool name --> | |
| 4 <description> Calculate SNP densities along chromosome from a VCF input</description> | |
| 5 | |
| 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> | |
| 7 <requirements> | |
| 8 <requirement type="binary">perl</requirement> | |
| 9 <requirement type="package" version="1.6.924">perl-bioperl</requirement> | |
| 10 <requirement type="package" version="0.1.14">vcftools</requirement> | |
| 11 <requirement type="package" version="0.1.14">perl-vcftools-vcf</requirement> | |
| 12 </requirements> | |
| 13 | |
| 14 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
| 15 <stdio> | |
| 16 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
| 17 <exit_code range="1:" level="fatal" /> | |
| 18 </stdio> | |
| 19 | |
| 20 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | |
| 21 <version_command> | |
| 22 <!-- | |
| 23 tool_binary -v | |
| 24 --> | |
| 25 </version_command> | |
| 26 | |
| 27 <!-- [REQUIRED] The command to execute --> | |
| 28 <command interpreter="bash"> | |
| 29 calculateSlidingWindowsSNPdensitiesFromVCF.sh $filein $fileout $fileout_bysample $step | |
| 30 </command> | |
| 31 | |
| 32 <!-- [REQUIRED] Input files and tool parameters --> | |
| 33 <inputs> | |
| 34 <param name="filein" type="data" format="vcf" optional="false" label="VCF input" /> | |
| 35 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> | |
| 36 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> | |
| 37 </inputs> | |
| 38 | |
| 39 <!-- [REQUIRED] Output files --> | |
| 40 <outputs> | |
| 41 <data name="fileout" format="txt" label="${fileout_label}" /> | |
| 42 <data name="fileout_bysample" format="txt" label="${fileout_label}.by_sample" /> | |
| 43 </outputs> | |
| 44 | |
| 45 <tests> | |
| 46 <test> | |
| 47 <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" /> | |
| 48 <param name="step" value="20000" /> | |
| 49 <output name="fileout" file="SNPden-result.txt" /> | |
| 50 <output name="fileout_bysample" file="SNPden-result_bysample.txt" /> | |
| 51 </test> | |
| 52 <!-- [HELP] Multiple tests can be defined with different parameters --> | |
| 53 <!-- | |
| 54 <test> | |
| 55 </test> | |
| 56 --> | |
| 57 </tests> | |
| 58 | |
| 59 <!-- [OPTIONAL] Help displayed in Galaxy --> | |
|
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60 <help><![CDATA[ |
| 9 | 61 |
| 62 .. class:: infomark | |
| 63 | |
| 64 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform | |
| 65 | |
| 66 | **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). | |
| 67 | |
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68 .. class:: infomark |
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69 |
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70 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) |
| 9 | 71 |
| 72 .. class:: infomark | |
| 73 | |
|
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74 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr |
| 9 | 75 |
| 76 --------------------------------------------------- | |
| 77 | |
| 78 ============= | |
| 79 SNP densities | |
| 80 ============= | |
| 81 | |
| 82 ----------- | |
| 83 Description | |
| 84 ----------- | |
| 85 | |
| 86 Calculate SNP densities along chromosome from a VCF file | |
| 87 | |
|
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88 ------------ |
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89 Dependencies |
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90 ------------ |
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91 VCFtools |
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92 vcftools_ 0.1.14, Conda version |
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93 VCFtools Perl libraries |
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94 perl-vcftools-vcf_ 0.1.14, Conda version |
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95 Bioperl |
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96 perl-bioperl_ 1.6.924, Conda version |
| 9 | 97 |
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98 .. _vcftools: https://anaconda.org/bioconda/vcftools |
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99 .. _perl-vcftools-vcf: https://anaconda.org/bioconda/perl-vcftools-vcf |
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100 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl |
| 9 | 101 |
| 102 ---------- | |
| 103 Input file | |
| 104 ---------- | |
| 105 | |
| 106 VCF file | |
| 107 File with SNPs | |
| 108 | |
| 109 ---------- | |
| 110 Parameters | |
| 111 ---------- | |
| 112 | |
| 113 Step | |
| 114 Step in bp for the window to calculate SNP density | |
| 115 | |
| 116 Output name | |
| 117 Output base name for the two ouput files | |
| 118 | |
| 119 ------------ | |
| 120 Output files | |
| 121 ------------ | |
| 122 | |
| 123 Output_name | |
| 124 Tabular file with SNP density in each postion | |
| 125 | |
| 126 Output_name.by_sample | |
| 127 Tabular file with SNP density for each sample | |
| 128 | |
| 129 --------------------------------------------------- | |
| 130 | |
| 131 --------------- | |
| 132 Working example | |
| 133 --------------- | |
| 134 | |
|
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135 Input file |
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136 ========== |
| 9 | 137 |
| 138 vcf file | |
| 139 ----------- | |
| 140 | |
| 141 :: | |
| 142 | |
| 143 #fileformat=VCFv4.1 | |
| 144 #FILTER=<ID=LowQual,Description="Low quality"> | |
| 145 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> | |
| 146 [...] | |
| 147 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CATB1 | |
| 148 chr1 2209 . G T 213.84 . AC=2;AF=1.00;AN=2;DP=7;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.50;MQ0=0;QD=30.55;EFF=DOWNSTREAM(MODIFIER||||Cc01g00020|mRNA||GSCOCT00012438001|),UPSTREAM(MODIFIER||||Cc01g00010|mRNA||GSCOCT00012439001|) GT:AD:DP:GQ:PL 1/1:0,7:7:18:242,18,0 | |
| 149 | |
| 150 Parameters | |
| 151 ========== | |
| 152 | |
| 153 Step -> 200000 | |
| 154 | |
| 155 Output name -> densities | |
| 156 | |
| 157 | |
| 158 Output files | |
| 159 ============ | |
| 160 | |
| 161 densities | |
| 162 --------- | |
| 163 | |
| 164 :: | |
| 165 | |
| 166 Chromosome Position SNPs | |
| 167 chr1 200000 355 | |
| 168 chr1 400000 228 | |
| 169 chr1 600000 63 | |
| 170 chr1 800000 191 | |
| 171 | |
| 172 | |
| 173 densities.by_sample | |
| 174 ------------------- | |
| 175 | |
| 176 :: | |
| 177 | |
| 178 Chromosome BA58 BA59 BD54 | |
| 179 chr1 220 197 225 | |
| 180 chr1 130 119 133 | |
| 181 chr1 43 43 40 | |
| 182 chr1 139 167 141 | |
| 183 | |
|
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184 ]]></help> |
| 9 | 185 <citations> |
| 186 <!-- [HELP] As DOI or BibTex entry --> | |
| 187 <citation type="bibtex">@article{Dereeper03062015, | |
| 188 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}, | |
| 189 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations}, | |
| 190 year = {2015}, | |
| 191 doi = {10.1093/nar/gkv351}, | |
| 192 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.}, | |
| 193 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract}, | |
| 194 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html}, | |
| 195 journal = {Nucleic Acids Research} | |
| 196 } | |
| 197 | |
| 198 </citation> | |
| 199 | |
| 200 </citations> | |
| 201 </tool> |