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1 <tool id="annotationStatsFromVCF" name="Get annotation statistics" version="1.0.0">
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2 <description> from VCF file </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="0.1.12b">vcftools</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command interpreter="perl">
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11 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 $output_stats_location
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12 </command>
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13 <inputs>
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14 <param type="data" name="input" format="vcf" label="VCF file" />
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15 <param type="text" name="output_label" label="Output_label" value='VCF_stats' />
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16 </inputs>
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17 <outputs>
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18 <data name="output_count" format="txt" label="${output_label}."/>
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19 <data name="output_stats_effect" format="txt" label="${output_label}."/>
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20 <data name="output_stats_location" format="txt" label="${output_label}."/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" value="vcf2fastaAndHapmap-sample.vcf"/>
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25 <output name="output_count" file="vcf2fastaAndHapmap-sample.vcf"/>
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26 <output name="output_stats_effect" file="vcf2fastaAndHapmap-sample.vcf"/>
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27 <output name="output_stats_location" file="vcf2fastaAndHapmap-sample.vcf"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31
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32 .. class:: infomark
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33
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34 **Authors** Dereeper Alexis (alexis.dereeper@ird.fr), IRD, South Green platform
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35
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36 | **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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37
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38 .. class:: infomark
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39
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40 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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41
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42 .. class:: infomark
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43
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44 **Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr
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45
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46 ---------------------------------------------------
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47
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48 ==============================
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49 Get Haplotypes From Phased VCF
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50 ==============================
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51
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52 -----------
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53 Description
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54 -----------
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55
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56 | Get Haplotype from phased VCF
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57
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58 -----------------
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59 Workflow position
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60 -----------------
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61
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62 **Upstream tool**
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63
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64 =============== ========================== =======
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65 Name output file(s) format
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66 =============== ========================== =======
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67 Beagle Phased VCF file VCF
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68 =============== ========================== =======
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69
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70
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71 **Downstream tool**
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72
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73 =============== ========================== ===========
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74 Name input file(s) format
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75 =============== ========================== ===========
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76 =============== ========================== ===========
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77
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78
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79 ----------
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80 Input file
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81 ----------
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82
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83 VCF file
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84 Phased VCF file
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85
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86 ----------
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87 Parameters
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88 ----------
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89
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90 Output file basename
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91 Prefix for the output VCF file
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92
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93 ------------
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94 Output files
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95 ------------
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96
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97
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98 Text file
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99 File describing haplotypes
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100
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101 Fasta file
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102 Fasta file with haplotypes
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103
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104 ---------------------------------------------------
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105
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106 ---------------
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107 Working example
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108 ---------------
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109
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110 Input files
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111 ===========
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112
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113 VCF file
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114 ---------
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115
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116 ::
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117
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118 #fileformat=VCFv4.1
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119 #FILTER=<ID=LowQual,Description="Low quality">
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120 #FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
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121 [...]
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122 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AZUCENA
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123 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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124
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125
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126 Parameters
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127 ==========
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128
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129 Output name -> haplotypes
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130
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131
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132 Output files
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133 ============
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134
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135 haplotypes.distinct_haplotypes.txt
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136 ----------------------------------
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137
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138 ::
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139
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140 ===Chr10===
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141 haplo1:2:CIRAD403_1,CIRAD403_2,
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142 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
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143 haplo2:2:MAHAE_1,MAHAE_2,
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144 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
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145
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146
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147 haplotypes.haplo.fas
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148 --------------------
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149
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150 ::
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151
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152 >Chr10_AZUCENA_1
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153 TTTAAGAAATTCCTATATAGGTCTTCTAAGCGTATCTATTAACAT
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154 >Chr10_AZUCENA_2
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155 TAAATCTTGGTGCTGATCTGATATTTAATGCGT
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156
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157 ]]></help>
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158 <citations>
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159 <!-- [HELP] As DOI or BibTex entry -->
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160 <citation type="bibtex">@article{Dereeper03062015,
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161 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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162 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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163 year = {2015},
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164 doi = {10.1093/nar/gkv351},
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165 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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166 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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167 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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168 journal = {Nucleic Acids Research}
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169 }
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170
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171 }</citation>
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172
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173 </citations>
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174
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175 </tool>
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