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annotate tassel.xml @ 6:28c0efb3a226 draft

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author dereeper
date Mon, 11 Dec 2023 15:12:25 +0000
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1 <tool id="Tassel" name="Tassel" version="2.0.0">
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2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
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3 <requirements>
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4 <requirement type="package" version="5.2.40">tassel</requirement>
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5 <requirement type="package" version="1.8">openjdk</requirement>
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6 </requirements>
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7 ​
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8 <stdio>
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9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12 ​
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13 <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
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14 #if $analysis_opts.fonction_selector == "mlm":
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15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
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16 -fork2 -r $analysis_opts.trait
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17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
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19 #end if
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20 -fork4 -k $analysis_opts.kinship
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21 -combineA -input1 -input2
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22 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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23 -input3
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24 #end if
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25 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
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26 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
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27 -runfork3
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28 #end if
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29 -runfork4
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30
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31 #else if $analysis_opts.fonction_selector == "glm":
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32 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
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33 -fork2 -r $analysis_opts.trait
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34 #if $analysis_opts.add_file.additional_file_selector == "yes":
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35 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
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36 #end if
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37 -combineA -input1 -input2
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38 #if $analysis_opts.add_file.additional_file_selector == "yes":
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39 -input3
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40 #end if
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41 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
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42 #if $analysis_opts.add_file.additional_file_selector == "yes":
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43 -runfork3
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44 #end if
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45 #else if $analysis_opts.fonction_selector == "ld":
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46 -fork1 -h $hapmap
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47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
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48 #else if $analysis_opts.fonction_selector == "ck":
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49 -fork1 -h $hapmap
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50 -ck -export tmpdir$$/kinship -runfork1
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51 #end if
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52 ]]></command>
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53 <inputs>
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54 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
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55 <conditional name="analysis_opts">
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56 <param name="fonction_selector" type="select" label="Type of analysis">
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57 <option value="mlm" selected="True">MLM</option>
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58 <option value="glm">GLM</option>
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59 <option value="ld">Linkage Disequilibrium</option>
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60 <option value="ck">Kinship</option>
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61 </param>
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62 <when value="glm">
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63 <param format="txt" name="trait" type="data" label="Trait file"/>
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64 <conditional name="add_file">
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65 <param name="additional_file_selector" type="select" label="Add structure file">
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66 <option value="no" selected="True">no</option>
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67 <option value="yes">yes</option>
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68 </param>
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69 <when value="yes">
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70 <param format="txt" name="structure" type="data" label="Structure file"/>
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71 </when>
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72 <when value="no">
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73 </when>
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74 </conditional>
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75 </when>
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76 <when value="mlm">
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77 <param format="txt" name="trait" type="data" label="Trait file"/>
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78 <param format="txt" name="kinship" type="data" label="Kinship file"/>
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79 <conditional name="add_structure_file">
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80 <param name="additional_file_selector" type="select" label="Add structure file">
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81 <option value="no" selected="True">no</option>
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82 <option value="yes">yes</option>
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83 </param>
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84 <when value="yes">
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85 <param format="txt" name="structure" type="data" label="Structure file"/>
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86 </when>
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87 <when value="no">
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88 </when>
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89 </conditional>
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90 <param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
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91 <option value="P3D" selected="True">P3D</option>
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92 <option value="EachMarker">EachMarker</option>
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93 </param>
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94 <param name="mlmCompressionLevel" type="select" label="Compression Level">
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95 <option value="Optimum" selected="True">Optimum</option>
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96 <option value="Custom">Custom</option>
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97 <option value="None">None</option>
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98 </param>
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99 </when>
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100 <when value="ld"></when>
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101 <when value="ck"></when>
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102 </conditional>
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103 <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
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104 </inputs>
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105 <outputs>
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106 <data format="txt" name="output1" label="Tassel output">
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107 <change_format>
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108 <when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
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109 </change_format>
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110 </data>
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111
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112 <data format="txt" name="output2" label="Allele effects">
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113 <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
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114 </data>
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115
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116 <data format="txt" name="output3" label="Compression file">
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117 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
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118 </data>
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119
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120 <data format="txt" name="log" label="Log file"/>
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121 </outputs>
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122 ​
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123 <tests>
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124 <test>
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125 <param name="hapmap" value="input_hapmap.txt"/>
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126 <conditional name="analysis_opts">
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127 <param name="fonction_selector" value="glm"/>
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128 <param name="trait" value="phenotyping_DRB.csv"/>
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129 <conditional name="add_structure_file">
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130 <param name="additional_file_selector" value="yes"/>
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131 <param name="structure" value="Best_K_Output"/>
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132 </conditional>
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133 </conditional>
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134 <param name="filterAlignMinFreq" value="0.05"/>
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135 <output name="output1" value="Tassel_output.txt"/>
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136 <output name="output2" value="Allele_effects.txt"/>
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137 </test>
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138 </tests>
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139 ​
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140 <help><![CDATA[
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141 ​
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142 ​
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143 .. class:: infomark
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144 ​
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145 **Tassel5** version 5.2.40
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146 ​
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147 .. class:: infomark
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148 ​
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149 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
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150 ​
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151 .. class:: infomark
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152 ​
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153 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
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154 ​
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155 ---------------------------------------------------
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156 ​
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157 =======
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158 Tassel5
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159 =======
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160 ​
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161 -----------
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162 Description
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163 -----------
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164 ​
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165 | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
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166 | For further informations on tassel, please visit the website_.
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167 ​
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168 .. _website: http://www.maizegenetics.net/tassel/
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169 ​
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170 ------------
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171 Dependencies
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172 ------------
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173 Tassel5
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174 tassel_ 5.2.40, Conda version
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175 ​
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176 .. _tassel: https://anaconda.org/bioconda/tassel
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177 ​
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178 ]]></help>
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179 <citations>
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180 <citation type="doi">10.1093/bioinformatics/btm308</citation>
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181 </citations>
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182 </tool>