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1 <tool id="sniplay_mdsplot" name="MDS plot" version="1.2.0">
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3
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> IBS matrix / multi-dimensional scaling</description>
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5
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6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
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7 <requirements>
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8 <requirement type="binary">perl</requirement>
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8
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9 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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10 <requirement type="package" version="1.90b4">plink</requirement>
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3
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11 </requirements>
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4
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12
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13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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14 <stdio>
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15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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16 <exit_code range="1:" level="fatal" />
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17 </stdio>
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18
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3
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19
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20 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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21 <version_command>
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22 <!--
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23 tool_binary -v
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24 -->
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25 </version_command>
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26
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27 <!-- [REQUIRED] The command to execute -->
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28 <command interpreter="bash">
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29 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log $groups
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30 </command>
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31
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32 <!-- [REQUIRED] Input files and tool parameters -->
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33 <inputs>
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34 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
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35 <param name="filemap" type="data" format="txt" optional="false" label="MAP input" help="4 columns tabular file: chromosome, snp id, genetic distance, bp position"/>
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36 <param name="groups" type="data" format="txt" optional="true" label="Groups" help="Groups defined by sNMF"/>
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37 <param name="fileout_label" type="text" value="analyse" label="Output name" help="Output name for tabular files" />
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38 </inputs>
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39
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40 <!-- [REQUIRED] Output files -->
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41 <outputs>
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42 <data name="fileout_matrix" type="data" format="txt" label="${fileout_label}.ibs_matrix.txt" />
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43 <data name="fileout_plot" type="data" format="txt" label="${fileout_label}.mds_plot.txt" />
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44 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
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45 </outputs>
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46
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47 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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48 <tests>
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49 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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50
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51 <test>
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52 <param name="fileped" value="MDSplot-input.ped" />
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53 <param name="filemap" value="MDSplot-input.map" />
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54 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" />
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55 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" />
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3
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56 </test>
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57
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58 <!-- [HELP] Multiple tests can be defined with different parameters -->
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59 <!--
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60 <test>
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61 </test>
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62 -->
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63 </tests>
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64
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65 <!-- [OPTIONAL] Help displayed in Galaxy -->
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66 <help>
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67
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68
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69 .. class:: infomark
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70
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71 **Authors** plink_
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72
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73 .. _plink: http://pngu.mgh.harvard.edu/purcell/plink/
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74
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75 | "PLINK: a toolset for whole-genome association and population-based linkage analysis.", **Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC.**, American Journal of Human Genetics, 81, 2007.
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76
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77
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78 .. class:: infomark
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79
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80 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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81
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82 .. class:: infomark
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83
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84 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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85
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86 .. class:: infomark
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87
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88 **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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89
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90 ---------------------------------------------------
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91
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92
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93
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94 ========
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95 MDS plot
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96 ========
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97
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98 -----------
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99 Description
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100 -----------
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101
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102 Compute an IBS matrix and a multi-dimensional scaling.
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103
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104
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105 -----------------
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106 Workflow position
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107 -----------------
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108
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109 **Upstream tool**
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110
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111 =============== ========================== ===============
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112 Name output file(s) format
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113 =============== ========================== ===============
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114 VCFtools Filter PED and MAP file tabular and MAP
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115 =============== ========================== ===============
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116
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117
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118
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119 ----------
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120 Input file
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121 ----------
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122
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123 PED file
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124
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125 MAP file
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126 4 columns tabular file: chromosome, snp id, genetic distance, bp position
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127
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128
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129 ----------
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130 Parameters
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131 ----------
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132
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133 Output name
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134 Output base name for the ouput files
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135
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136
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137 ------------
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138 Output files
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139 ------------
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140
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141 Output_name.ibs_matrix.txt
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142 Tabular file with IBS matrix
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143
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144 Output_name.mds_plot.txt
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145 File to construct mds plot
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146
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147 Output_name.log
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148 Log file
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149
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150 ------------
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151 Dependencies
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152 ------------
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153 plink
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154 version 1.07
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155
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156 ---------------------------------------------------
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157
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158 ---------------
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159 Working example
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160 ---------------
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161
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162 Input files
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163 ===========
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164
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165 PED file
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166 -----------
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167
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168 ::
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169
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170 IRAT112 1 0 0 1 1 1 1 4 4 ...
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171 IAC25 1 0 0 1 1 1 1 4 4 ...
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172 CIRAD409 1 0 0 1 1 3 3 1 1 ...
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173
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174
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175 MAP file
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176 -----------
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177
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178 ::
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179
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180 Chr1 Chr1:4299 0 4299
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181 Chr1 Chr1:26710 0 26710
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182 Chr1 Chr1:56184 0 56184
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183 Chr1 Chr1:93272 0 93272
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184
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185
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186
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187 Parameters
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188 ==========
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189
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190 Output name -> densities
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191
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192
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193 Output files
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194 ============
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195
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196 densities.ibs_matrix.txt
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197 ------------------------
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198
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199 ::
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200
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201 Individuals IRAT112 IAC25 IAC165 KARASUKARASURANKASU DOURADOPRECOCE ...
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202 IRAT112 1 0.93691 0.937407 0.734724 0.943368 ...
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203 IAC25 0.93691 1 0.958768 0.723299 0.965723 ...
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204
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205
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206 densities.mds_plot.txt
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207 ----------------------
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208
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209 ::
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210
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211 IRAT112 -0.0969382 0.0376036
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212 IAC25 -0.0918126 0.0501177
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213
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214
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215
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216 </help>
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217 <citations>
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218 <!-- [HELP] As DOI or BibTex entry -->
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219 <citation type="bibtex">@article{Dereeper03062015,
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220 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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221 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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222 year = {2015},
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223 doi = {10.1093/nar/gkv351},
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224 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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225 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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226 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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227 journal = {Nucleic Acids Research}
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228 }
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229
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230 </citation>
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231
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232 </citations>
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233
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234 </tool>
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