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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="2019.7">
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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="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8
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9
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10 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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12 #else:
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13 #set $tax_path = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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14 qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path $tax_path --output-path ref-taxonomy.qza;
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15 #set $tax='ref-taxonomy.qza'
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16 #end if
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17
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18
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19 qiime feature-classifier fit-classifier-naive-bayes
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20
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21
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22 --i-reference-taxonomy '$tax'
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23
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24
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25 --i-reference-reads=$ireferencereads
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26
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27 #if str($iclassweight) != 'None':
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28 --i-class-weight=$iclassweight
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29 #end if
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30
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31 #if str($pclassifyalpha):
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32 --p-classify--alpha=$pclassifyalpha
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33 #end if
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34
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35 #if str($pclassifychunksize):
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36 --p-classify--chunk-size=$pclassifychunksize
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37 #end if
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38
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39
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40
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41
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42 #if '__sq__' in str($pclassifyclassprior):
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43 #set $pclassifyclassprior_temp = $pclassifyclassprior.replace('__sq__', "'")
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44 #set $pclassifyclassprior = $pclassifyclassprior_temp
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45 #end if
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46
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47 #if str($pclassifyclassprior):
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48 --p-classify--class-prior="$pclassifyclassprior"
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49 #end if
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50
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51
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52
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53
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54 #if $pclassifyfitprior:
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55 --p-classify--fit-prior
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56 #end if
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57
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58 #if $pfeatextalternatesign:
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59 --p-feat-ext--alternate-sign
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60 #end if
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61
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62
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63
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64
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65
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66 #if '__sq__' in str($pfeatextanalyzer):
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67 #set $pfeatextanalyzer_temp = $pfeatextanalyzer.replace('__sq__', "'")
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68 #set $pfeatextanalyzer = $pfeatextanalyzer_temp
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69 #end if
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70
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71 #if str($pfeatextanalyzer):
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72 --p-feat-ext--analyzer="$pfeatextanalyzer"
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73 #end if
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74
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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 #if $pfeatextbinary:
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80 --p-feat-ext--binary
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81 #end if
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82
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83
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84
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85 #if '__sq__' in str($pfeatextdecodeerror):
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86 #set $pfeatextdecodeerror_temp = $pfeatextdecodeerror.replace('__sq__', "'")
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87 #set $pfeatextdecodeerror = $pfeatextdecodeerror_temp
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88 #end if
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89
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90 #if str($pfeatextdecodeerror):
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91 --p-feat-ext--decode-error="$pfeatextdecodeerror"
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92 #end if
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93
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94
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95
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96
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97
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98 #if '__sq__' in str($pfeatextencoding):
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99 #set $pfeatextencoding_temp = $pfeatextencoding.replace('__sq__', "'")
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100 #set $pfeatextencoding = $pfeatextencoding_temp
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101 #end if
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102
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103 #if str($pfeatextencoding):
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104 --p-feat-ext--encoding="$pfeatextencoding"
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105 #end if
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106
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107
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108
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109
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110
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111 #if '__sq__' in str($pfeatextinput):
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112 #set $pfeatextinput_temp = $pfeatextinput.replace('__sq__', "'")
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113 #set $pfeatextinput = $pfeatextinput_temp
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114 #end if
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115
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116 #if str($pfeatextinput):
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117 --p-feat-ext--input="$pfeatextinput"
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118 #end if
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119
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120
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121
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122
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123 #if $pnofeatextlowercase:
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124 --p-no-feat-ext--lowercase
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125 #end if
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126
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127 #if str($pfeatextnfeatures):
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128 --p-feat-ext--n-features=$pfeatextnfeatures
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129 #end if
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130
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131
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132
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133
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134 #if '__sq__' in str($pfeatextngramrange):
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135 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
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136 #set $pfeatextngramrange = $pfeatextngramrange_temp
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137 #end if
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138
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139 #if '__ob__' in str($pfeatextngramrange):
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140 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
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141 #set $pfeatextngramrange = $pfeatextngramrange_temp
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142 #end if
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143 #if 'X' in str($pfeatextngramrange):
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144 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
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145 #set $pfeatextngramrange = $pfeatextngramrange_temp
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146 #end if
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147
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148 #if str($pfeatextngramrange):
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149 --p-feat-ext--ngram-range="$pfeatextngramrange"
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150 #end if
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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
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156 #if $pfeatextnonnegative:
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157 --p-feat-ext--non-negative
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158 #end if
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159
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160
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161 #if '__sq__' in str($pfeatextnorm):
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162 #set $pfeatextnorm_temp = $pfeatextnorm.replace('__sq__', "'")
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163 #set $pfeatextnorm = $pfeatextnorm_temp
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164 #end if
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165
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166 #if str($pfeatextnorm):
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167 --p-feat-ext--norm="$pfeatextnorm"
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168 #end if
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169
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170
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171
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172
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173 #if '__sq__' in str($pfeatextpreprocessor):
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174 #set $pfeatextpreprocessor_temp = $pfeatextpreprocessor.replace('__sq__', "'")
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175 #set $pfeatextpreprocessor = $pfeatextpreprocessor_temp
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176 #end if
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177
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178 #if str($pfeatextpreprocessor):
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179 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
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180 #end if
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181
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182
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183
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184
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185 #if '__sq__' in str($pfeatextstopwords):
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186 #set $pfeatextstopwords_temp = $pfeatextstopwords.replace('__sq__', "'")
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187 #set $pfeatextstopwords = $pfeatextstopwords_temp
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188 #end if
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189
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190 #if str($pfeatextstopwords):
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191 --p-feat-ext--stop-words="$pfeatextstopwords"
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192 #end if
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193
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194
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195
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196
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197
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198 #if '__sq__' in str($pfeatextstripaccents):
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199 #set $pfeatextstripaccents_temp = $pfeatextstripaccents.replace('__sq__', "'")
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200 #set $pfeatextstripaccents = $pfeatextstripaccents_temp
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201 #end if
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202
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203 #if str($pfeatextstripaccents):
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204 --p-feat-ext--strip-accents="$pfeatextstripaccents"
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205 #end if
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206
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207
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208
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209
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210
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211
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212 #if '__sq__' in str($pfeatexttokenpattern):
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213 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
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214 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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215 #end if
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216
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217 #if '__ob__' in str($pfeatexttokenpattern):
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218 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
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219 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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220 #end if
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221
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222 #if 'X' in str($pfeatexttokenpattern):
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223 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
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224 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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225 #end if
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226
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227 #if str($pfeatexttokenpattern):
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228 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
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229 #end if
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230
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231
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232
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233
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234
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235 #if '__sq__' in str($pfeatexttokenizer):
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236 #set $pfeatexttokenizer_temp = $pfeatexttokenizer.replace('__sq__', "'")
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237 #set $pfeatexttokenizer = $pfeatexttokenizer_temp
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238 #end if
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239
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240 #if str($pfeatexttokenizer):
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241 --p-feat-ext--tokenizer="$pfeatexttokenizer"
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242 #end if
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243
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244 --o-classifier=oclassifier
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245 ;
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246 cp oclassifier.qza $oclassifier
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247 ]]></command>
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248 <inputs>
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249 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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250 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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251
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252 <conditional name="id_to_taxonomy_fp" optional="True">
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253 <param name="selector" type="select" label="Reference taxonomy to query">
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254 <option value="cached">Public databases</option>
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255 <option value="history">Databases from your history</option>
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256 </param>
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257 <when value="cached">
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258 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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259 <options from_data_table="qiime_taxonomy" />
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260 </param>
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261 </when>
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262 <when value="history">
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263 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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264 </when>
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265 </conditional>
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266
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267 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
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268 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
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269 <param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="null"/>
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270 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
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271 <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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272 <param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
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273 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
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274 <param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
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275 <param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
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276 <param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="content"/>
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277 <param label="--p-no-feat-ext--lowercase: [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
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278 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
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279 <param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="[7, 7]"/>
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280 <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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281 <param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="l2"/>
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282 <param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
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283 <param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="null"/>
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284 <param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
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285 <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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286 <param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
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287 </inputs>
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288 <outputs>
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289 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
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290 </outputs>
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291 <help><![CDATA[
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292 Train the naive_bayes classifier
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293 ################################
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294
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295 Create a scikit-learn naive_bayes classifier for reads
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296
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297 Parameters
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298 ----------
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299 reference_reads : FeatureData[Sequence]
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300 \
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301
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302 reference_taxonomy : FeatureData[Taxonomy]
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303 \
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304
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305 class_weight : FeatureTable[RelativeFrequency], optional
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306 \
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307
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308 classify__alpha : Float, optional
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309 \
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310
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311 classify__chunk_size : Int, optional
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312 \
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313
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314 classify__class_prior : Str, optional
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315 \
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316
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317 classify__fit_prior : Bool, optional
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318 \
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319
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320 feat_ext__alternate_sign : Bool, optional
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321 \
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322
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323 feat_ext__analyzer : Str, optional
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324 \
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325
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326 feat_ext__binary : Bool, optional
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327 \
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328
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329 feat_ext__decode_error : Str, optional
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330 \
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331
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332 feat_ext__encoding : Str, optional
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333 \
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334
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335 feat_ext__input : Str, optional
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336 \
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337
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338 feat_ext__lowercase : Bool, optional
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339 \
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340
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341 feat_ext__n_features : Int, optional
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342 \
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343
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344 feat_ext__ngram_range : Str, optional
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345 \
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346
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347 feat_ext__non_negative : Bool, optional
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348 \
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349
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350 feat_ext__norm : Str, optional
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351 \
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352
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353 feat_ext__preprocessor : Str, optional
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354 \
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355
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356 feat_ext__stop_words : Str, optional
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357 \
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358
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359 feat_ext__strip_accents : Str, optional
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360 \
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361
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362 feat_ext__token_pattern : Str, optional
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363 \
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364
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365 feat_ext__tokenizer : Str, optional
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366 \
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367
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368 Returns
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369 -------
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370 classifier : TaxonomicClassifier
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371 \
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372
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373 ]]></help>
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374 <macros>
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375 <import>qiime_citation.xml</import>
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376 </macros>
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377 <expand macro="qiime_citation"/>
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378 </tool>
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