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1 <tool id="sniplay_rooting" name="Rooting" version="1.0.3">
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2
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3 <!-- [REQUIRED] Tool description displayed after the tool name -->
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4 <description> Midpoint rooting of newick tree </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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9 <requirement type="package">Rootings_54.jar</requirement>
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10 </requirements>
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11
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12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
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13 <stdio>
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14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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15 <exit_code range="1:" level="fatal" />
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16 </stdio>
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17
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18
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19 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
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20 <version_command>
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21 <!--
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22 tool_binary -v
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23 -->
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24 </version_command>
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25
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26 <!-- [REQUIRED] The command to execute -->
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27 <command interpreter="perl">
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28 Rooting.pl -i $filein -o $fileout && mv ${filein}.rooting.log $fileout_log
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29 </command>
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30
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31 <!-- [REQUIRED] Input files and tool parameters -->
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32 <inputs>
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33 <param name="filein" type="data" format="nwk" optional="false" label="Fasta alignment input" />
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34 <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" />
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35 </inputs>
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36
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37 <!-- [REQUIRED] Output files -->
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38 <outputs>
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39 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
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40 <data name="fileout" type="data" format="nwk" label="${fileout_label}" />
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41 </outputs>
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42
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43 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
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44 <tests>
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45 <!-- [HELP] Test files have to be in the ~/test-data directory -->
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46
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47 <test>
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48 <param name="filein" value="rooting-newick" />
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49 <output name="fileout" file="rooting-out_tree" />
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50 </test>
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51
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52 <!-- [HELP] Multiple tests can be defined with different parameters -->
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53 <!--
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54 <test>
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55 </test>
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56 -->
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57 </tests>
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58
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59 <!-- [OPTIONAL] Help displayed in Galaxy -->
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60 <help>
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61
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62
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63 .. class:: infomark
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64
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65 **Authors** Jean-François Dufayard, CIRAD, South Green platform
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66
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67
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68 .. class:: infomark
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69
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70 **Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique.
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71
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72 .. class:: infomark
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73
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74 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
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75
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76 .. class:: infomark
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77
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78 **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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79
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80 ---------------------------------------------------
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81
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82
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83
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84
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85 =======
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86 Rooting
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87 =======
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88
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89 -----------
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90 Description
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91 -----------
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92
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93 Compute a midpoint newick rooted tree.
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94
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95
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96 -----------------
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97 Workflow position
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98 -----------------
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99
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100 **Upstream tool**
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101
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102 =========== ========================== =======
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103 Name output file(s) format
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104 =========== ========================== =======
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105 fastme Newick tree Newick
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106 =========== ========================== =======
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107
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108
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109
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110 ----------
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111 Input file
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112 ----------
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113
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114 Newick file
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115
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116
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117 ----------
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118 Parameters
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119 ----------
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120
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121 Output name
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122 Output base name for the ouput files
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123
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124
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125 ------------
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126 Output files
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127 ------------
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128
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129 Output_name
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130 Resulting tree rooted in newick format
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131
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132 Output_name.log
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133 Log file
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134
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135 ------------
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136 Dependencies
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137 ------------
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138 Rooting
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139 CIRAD tool. Contact jean-francois.dufayard@cirad.fr
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140
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141 ---------------------------------------------------
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142
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143 ---------------
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144 Working example
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145 ---------------
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146
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147 Input files
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148 ===========
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149
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150 Newick file
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151 -----------
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152
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153 ::
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154
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155 (((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267, ...
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156
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157
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158 Parameters
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159 ==========
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160
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161 Output name -> out tree
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162
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163
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164 Output files
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165 ============
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166
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167 out tree
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168 --------
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169
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170 ::
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171
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172 (ref:0.9384270000000001,(((((((((((((((((((((((((((((((((((IRAT257:0.044246,IRAT112:0.023421):0.009006,ARAGUAIA:0.093061):0.004662...
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173
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174
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175 </help>
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176 <citations>
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177 <!-- [HELP] As DOI or BibTex entry -->
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178 <citation type="bibtex">@article{Dereeper03062015,
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179 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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180 title = {SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations},
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181 year = {2015},
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182 doi = {10.1093/nar/gkv351},
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183 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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184 URL = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.abstract},
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185 eprint = {http://nar.oxfordjournals.org/content/early/2015/06/03/nar.gkv351.full.pdf+html},
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186 journal = {Nucleic Acids Research}
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187 }
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188
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189 </citation>
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190
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191 </citations>
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192
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193 </tool>
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