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

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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>
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3 <requirements>
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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>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command interpreter="perl">
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12 AnnotationStatsFromVCF.pl -v $input -o $output_label -s $step &amp;&amp; mv ${output_label} $output_count &amp;&amp; mv ${output_label}.effect $output_stats_effect &amp;&amp; mv ${output_label}.location $output_stats_location
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13 </command>
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14 <inputs>
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15 <param type="data" name="input" format="vcf" label="VCF file" />
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16 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
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17 <param type="text" name="output_label" label="Output_label" value='VCF_stats' optional='false' />
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18 </inputs>
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19 <outputs>
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20 <data name="output_count" format="txt" label="${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"/>
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23 </outputs>
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24 <tests>
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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"/>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34
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35 .. class:: infomark
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36
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37 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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38
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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).
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40
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41 .. class:: infomark
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42
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43 **Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA)
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44
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45 .. class:: infomark
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46
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47 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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48
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49 ---------------------------------------------------
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50
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51 =========================
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52 Get annotation statistics
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53 =========================
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54
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55 -----------
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56 Description
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57 -----------
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58
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59 | Get annotation statistics from VCF
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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
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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
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71
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72 ----------
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73 Input file
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74 ----------
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75
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76 VCF file
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77 VCF file
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78
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79 ----------
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80 Parameters
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81 ----------
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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
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88
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89 ------------
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90 Output files
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91 ------------
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92
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93 Output_name
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94
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95 Output_name.effect file
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96
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97 Output_name.location file
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98
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99 ---------------------------------------------------
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100
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101 ---------------
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102 Working example
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103 ---------------
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104
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105 Input file
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106 ==========
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107
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108 VCF file
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109 ---------
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110
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111 ::
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112
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113 #fileformat=VCFv4.1
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114 #FILTER=&lt;ID=LowQual,Description="Low quality">
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115 #FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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116 [...]
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117 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA
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118 Chr1 4299 . G A . PASS AR2=1;DR2=1;AF=0.168 GT:DS:GP 0|0:0:1,0,0
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119
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120
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121 Parameters
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122 ==========
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123
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124 Step -> 50000
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125 Output label -> VCF_stats
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127
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128 Output files
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129 ============
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130
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131 VCF_stats
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132 ----------------------------------
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133
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134 ::
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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
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142 VCF_stats.effect
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143 --------------------
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144
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145 ::
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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
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160 ]]></help>
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161 <citations>
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162 <!-- [HELP] As DOI or BibTex entry -->
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163 <citation type="bibtex">@article{Dereeper03062015,
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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},
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165 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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166 year = {2015},
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167 doi = {10.1093/nar/gkv351},
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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.},
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169 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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170 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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171 journal = {Nucleic Acids Research}
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172 }
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173
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174 }</citation>
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175
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176 </citations>
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177
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178 </tool>