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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" version="2019.4">
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3 <description> - Train the naive_bayes classifier</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-classifier fit-classifier-naive-bayes
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9
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10 --i-reference-reads=$ireferencereads
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11
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12
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13 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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15 --i-reference-taxonomy '$tax'
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16 #else:
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17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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18 --i-reference-taxonomy '$tax'
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19 #end if
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20
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21
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22 #if str($iclassweight) != 'None':
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23 --i-class-weight=$iclassweight
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24 #end if
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25
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26 #if $pclassifyalpha:
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27 --p-classify--alpha=$pclassifyalpha
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28 #end if
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29
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30 #if $pclassifychunksize:
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31 --p-classify--chunk-size=$pclassifychunksize
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32 #end if
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33
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34
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35
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36
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37 #if '__sq__' in str($pclassifyclassprior):
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38 #set $pclassifyclassprior_temp = $pclassifyclassprior.replace('__sq__', "'")
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39 #set $pclassifyclassprior = $pclassifyclassprior_temp
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40 #end if
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41
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42 #if str($pclassifyclassprior):
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43 --p-classify--class-prior="$pclassifyclassprior"
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44 #end if
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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 #if $pclassifyfitprior:
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50 --p-classify--fit-prior
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51 #end if
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52
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53 #if $pfeatextalternatesign:
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54 --p-feat-ext--alternate-sign
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55 #end if
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56
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57
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58
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59
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60
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61 #if '__sq__' in str($pfeatextanalyzer):
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62 #set $pfeatextanalyzer_temp = $pfeatextanalyzer.replace('__sq__', "'")
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63 #set $pfeatextanalyzer = $pfeatextanalyzer_temp
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64 #end if
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65
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66 #if str($pfeatextanalyzer):
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67 --p-feat-ext--analyzer="$pfeatextanalyzer"
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68 #end if
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69
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70
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71
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72
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73
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74 #if $pfeatextbinary:
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75 --p-feat-ext--binary
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76 #end if
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77
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78
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79
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80 #if '__sq__' in str($pfeatextdecodeerror):
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81 #set $pfeatextdecodeerror_temp = $pfeatextdecodeerror.replace('__sq__', "'")
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82 #set $pfeatextdecodeerror = $pfeatextdecodeerror_temp
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83 #end if
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84
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85 #if str($pfeatextdecodeerror):
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86 --p-feat-ext--decode-error="$pfeatextdecodeerror"
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87 #end if
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88
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89
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90
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91
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92
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93 #if '__sq__' in str($pfeatextencoding):
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94 #set $pfeatextencoding_temp = $pfeatextencoding.replace('__sq__', "'")
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95 #set $pfeatextencoding = $pfeatextencoding_temp
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96 #end if
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97
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98 #if str($pfeatextencoding):
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99 --p-feat-ext--encoding="$pfeatextencoding"
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100 #end if
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101
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102
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103
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104
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105
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106 #if '__sq__' in str($pfeatextinput):
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107 #set $pfeatextinput_temp = $pfeatextinput.replace('__sq__', "'")
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108 #set $pfeatextinput = $pfeatextinput_temp
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109 #end if
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110
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111 #if str($pfeatextinput):
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112 --p-feat-ext--input="$pfeatextinput"
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113 #end if
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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 #if $pnofeatextlowercase:
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119 --p-no-feat-ext--lowercase
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120 #end if
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121
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122 #if $pfeatextnfeatures:
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123 --p-feat-ext--n-features=$pfeatextnfeatures
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124 #end if
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125
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126
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127
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128
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129 #if '__sq__' in str($pfeatextngramrange):
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130 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
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131 #set $pfeatextngramrange = $pfeatextngramrange_temp
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132 #end if
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133
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134 #if '__ob__' in str($pfeatextngramrange):
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135 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
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136 #set $pfeatextngramrange = $pfeatextngramrange_temp
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137 #end if
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138 #if 'X' in str($pfeatextngramrange):
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139 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
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140 #set $pfeatextngramrange = $pfeatextngramrange_temp
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141 #end if
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142
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143 #if str($pfeatextngramrange):
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144 --p-feat-ext--ngram-range="$pfeatextngramrange"
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145 #end if
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146
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147
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148
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149
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150
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151 #if $pfeatextnonnegative:
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152 --p-feat-ext--non-negative
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153 #end if
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154
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155
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156 #if '__sq__' in str($pfeatextnorm):
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157 #set $pfeatextnorm_temp = $pfeatextnorm.replace('__sq__', "'")
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158 #set $pfeatextnorm = $pfeatextnorm_temp
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159 #end if
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160
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161 #if str($pfeatextnorm):
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162 --p-feat-ext--norm="$pfeatextnorm"
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163 #end if
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164
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165
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166
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167
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168 #if '__sq__' in str($pfeatextpreprocessor):
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169 #set $pfeatextpreprocessor_temp = $pfeatextpreprocessor.replace('__sq__', "'")
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170 #set $pfeatextpreprocessor = $pfeatextpreprocessor_temp
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171 #end if
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172
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173 #if str($pfeatextpreprocessor):
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174 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
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175 #end if
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176
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177
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178
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179
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180 #if '__sq__' in str($pfeatextstopwords):
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181 #set $pfeatextstopwords_temp = $pfeatextstopwords.replace('__sq__', "'")
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182 #set $pfeatextstopwords = $pfeatextstopwords_temp
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183 #end if
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184
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185 #if str($pfeatextstopwords):
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186 --p-feat-ext--stop-words="$pfeatextstopwords"
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187 #end if
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188
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189
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190
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191
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192
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193 #if '__sq__' in str($pfeatextstripaccents):
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194 #set $pfeatextstripaccents_temp = $pfeatextstripaccents.replace('__sq__', "'")
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195 #set $pfeatextstripaccents = $pfeatextstripaccents_temp
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196 #end if
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197
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198 #if str($pfeatextstripaccents):
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199 --p-feat-ext--strip-accents="$pfeatextstripaccents"
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200 #end if
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201
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202
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203
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204
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205
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206
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207 #if '__sq__' in str($pfeatexttokenpattern):
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208 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
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209 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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210 #end if
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211
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212 #if '__ob__' in str($pfeatexttokenpattern):
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213 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
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214 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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215 #end if
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216
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217 #if 'X' in str($pfeatexttokenpattern):
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218 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
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219 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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220 #end if
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221
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222 #if str($pfeatexttokenpattern):
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223 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
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224 #end if
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225
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226
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227
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228
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229
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230 #if '__sq__' in str($pfeatexttokenizer):
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231 #set $pfeatexttokenizer_temp = $pfeatexttokenizer.replace('__sq__', "'")
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232 #set $pfeatexttokenizer = $pfeatexttokenizer_temp
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233 #end if
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234
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235 #if str($pfeatexttokenizer):
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236 --p-feat-ext--tokenizer="$pfeatexttokenizer"
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237 #end if
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238
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239 --o-classifier=oclassifier
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240 ;
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241 cp oclassifier.qza $oclassifier
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242 ]]></command>
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243 <inputs>
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244 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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245 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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246
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247 <conditional name="id_to_taxonomy_fp" optional="True">
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248 <param name="selector" type="select" label="Reference taxonomy to query">
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249 <option value="cached">Public databases</option>
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250 <option value="history">Databases from your history</option>
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251 </param>
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252 <when value="cached">
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253 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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254 <options from_data_table="qiime_taxonomy" />
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255 </param>
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256 </when>
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257 <when value="history">
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258 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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259 </when>
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260 </conditional>
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261
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262 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
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263 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
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264 <param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="null"/>
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265 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
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266 <param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean"/>
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267 <param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
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268 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
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269 <param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
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270 <param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
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271 <param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="content"/>
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272 <param label="--p-no-feat-ext--lowercase: [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
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273 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
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274 <param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="[7, 7]"/>
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275 <param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" selected="False" type="boolean"/>
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276 <param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="l2"/>
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277 <param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
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278 <param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="null"/>
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279 <param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
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280 <param label="--p-feat-ext--token-pattern: TEXT [default: '(?u)\\b\\w\\w+\\b']" name="pfeatexttokenpattern" optional="True" type="text" value="(?u)\\b\\w\\w+\\b"/>
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281 <param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
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282 </inputs>
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283 <outputs>
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284 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
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285 </outputs>
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286 <help><![CDATA[
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287 Train the naive_bayes classifier
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288 ################################
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289
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290 Create a scikit-learn naive_bayes classifier for reads
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291
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292 Parameters
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293 ----------
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294 reference_reads : FeatureData[Sequence]
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295 \
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296
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297 reference_taxonomy : FeatureData[Taxonomy]
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298 \
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299
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300 class_weight : FeatureTable[RelativeFrequency], optional
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301 \
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302
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303 classify__alpha : Float, optional
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304 \
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305
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306 classify__chunk_size : Int, optional
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307 \
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308
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309 classify__class_prior : Str, optional
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310 \
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311
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312 classify__fit_prior : Bool, optional
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313 \
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314
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315 feat_ext__alternate_sign : Bool, optional
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316 \
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317
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318 feat_ext__analyzer : Str, optional
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319 \
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320
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321 feat_ext__binary : Bool, optional
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322 \
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323
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324 feat_ext__decode_error : Str, optional
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325 \
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326
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327 feat_ext__encoding : Str, optional
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328 \
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329
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330 feat_ext__input : Str, optional
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331 \
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332
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333 feat_ext__lowercase : Bool, optional
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334 \
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335
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336 feat_ext__n_features : Int, optional
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337 \
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338
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339 feat_ext__ngram_range : Str, optional
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340 \
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341
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342 feat_ext__non_negative : Bool, optional
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343 \
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344
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345 feat_ext__norm : Str, optional
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346 \
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347
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348 feat_ext__preprocessor : Str, optional
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349 \
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350
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351 feat_ext__stop_words : Str, optional
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352 \
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353
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354 feat_ext__strip_accents : Str, optional
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355 \
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356
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357 feat_ext__token_pattern : Str, optional
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358 \
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359
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360 feat_ext__tokenizer : Str, optional
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361 \
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362
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363 Returns
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364 -------
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365 classifier : TaxonomicClassifier
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366 \
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367
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368 ]]></help>
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369 <macros>
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370 <import>qiime_citation.xml</import>
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371 </macros>
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372 <expand macro="qiime_citation"/>
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373 </tool>
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