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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"
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3 version="2020.8">
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4 <description>Train the naive_bayes classifier</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime feature-classifier fit-classifier-naive-bayes
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10
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11 --i-reference-reads=$ireferencereads
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12
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13 --i-reference-taxonomy=$ireferencetaxonomy
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14
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15 #if str($iclassweight) != 'None':
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16 --i-class-weight=$iclassweight
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17 #end if
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18
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19 --p-classify--alpha=$pclassifyalpha
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20
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21 --p-classify--chunk-size=$pclassifychunksize
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22
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23 #if str($pclassifyclassprior):
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24 --p-classify--class-prior=$pclassifyclassprior
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25 #end if
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26 #if $pclassifyfitprior:
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27 --p-classify--fit-prior
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28 #end if
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29
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30 #if $pfeatextalternatesign:
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31 --p-feat-ext--alternate-sign
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32 #end if
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33
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34 #if str($pfeatextanalyzer):
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35 --p-feat-ext--analyzer=$pfeatextanalyzer
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36 #end if
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37 #if $pfeatextbinary:
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38 --p-feat-ext--binary
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39 #end if
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40
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41 #if str($pfeatextdecodeerror):
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42 --p-feat-ext--decode-error=$pfeatextdecodeerror
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43 #end if
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44 #if str($pfeatextencoding):
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45 --p-feat-ext--encoding=$pfeatextencoding
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46 #end if
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47 #if str($pfeatextinput):
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48 --p-feat-ext--input=$pfeatextinput
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49 #end if
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50 #if $pnofeatextlowercase:
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51 --p-no-feat-ext--lowercase
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52 #end if
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53
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54 --p-feat-ext--n-features=$pfeatextnfeatures
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55
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56 #if '__ob__' in str($pfeatextngramrange):
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57 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
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58 #set $pfeatextngramrange = $pfeatextngramrange_temp
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59 #end if
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60 #if '__cb__' in str($pfeatextngramrange):
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61 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__cb__', ']')
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62 #set $pfeatextngramrange = $pfeatextngramrange_temp
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63 #end if
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64 #if 'X' in str($pfeatextngramrange):
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65 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
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66 #set $pfeatextngramrange = $pfeatextngramrange_temp
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67 #end if
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68 #if '__sq__' in str($pfeatextngramrange):
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69 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
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70 #set $pfeatextngramrange = $pfeatextngramrange_temp
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71 #end if
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72 #if '__db__' in str($pfeatextngramrange):
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73 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__db__', '"')
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74 #set $pfeatextngramrange = $pfeatextngramrange_temp
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75 #end if
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76
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77 #if str($pfeatextngramrange):
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78 --p-feat-ext--ngram-range=$pfeatextngramrange
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79 #end if
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80
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81 #if str($pfeatextnorm):
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82 --p-feat-ext--norm=$pfeatextnorm
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83 #end if
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84 #if str($pfeatextpreprocessor):
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85 --p-feat-ext--preprocessor=$pfeatextpreprocessor
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86 #end if
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87 #if str($pfeatextstopwords):
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88 --p-feat-ext--stop-words=$pfeatextstopwords
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89 #end if
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90 #if str($pfeatextstripaccents):
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91 --p-feat-ext--strip-accents=$pfeatextstripaccents
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92 #end if
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93 #if '__ob__' in str($pfeatexttokenpattern):
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94 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
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95 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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96 #end if
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97 #if '__cb__' in str($pfeatexttokenpattern):
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98 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__cb__', ']')
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99 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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100 #end if
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101 #if 'X' in str($pfeatexttokenpattern):
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102 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
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103 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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104 #end if
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105 #if '__sq__' in str($pfeatexttokenpattern):
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106 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
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107 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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108 #end if
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109 #if '__db__' in str($pfeatexttokenpattern):
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110 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__db__', '"')
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111 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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112 #end if
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113
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114 #if str($pfeatexttokenpattern):
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115 --p-feat-ext--token-pattern=$pfeatexttokenpattern
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116 #end if
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117
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118 #if str($pfeatexttokenizer):
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119 --p-feat-ext--tokenizer=$pfeatexttokenizer
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120 #end if
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121 #if $pverbose:
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122 --p-verbose
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123 #end if
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124
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125 --o-classifier=oclassifier
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126
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127 #if str($examples) != 'None':
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128 --examples=$examples
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129 #end if
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130
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131 ;
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132 cp oclassifier.qza $oclassifier
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133
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134 ]]></command>
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135 <inputs>
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136 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data" />
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137 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" />
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138 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" />
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139 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001" />
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140 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000" />
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141 <param label="--p-classify--class-prior: TEXT [default: \'null\']" name="pclassifyclassprior" optional="False" type="text" value="\'null\'" />
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142 <param label="--p-classify--fit-prior: --p-classify--fit-prior: / --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean" />
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143 <param label="--p-feat-ext--alternate-sign: --p-feat-ext--alternate-sign: / --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean" />
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144 <param label="--p-feat-ext--analyzer: TEXT [default: \'char_wb\']" name="pfeatextanalyzer" optional="False" type="text" value="\'char_wb\'" />
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145 <param label="--p-feat-ext--binary: --p-feat-ext--binary: / --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean" />
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146 <param label="--p-feat-ext--decode-error: TEXT [default: \'strict\']" name="pfeatextdecodeerror" optional="False" type="text" value="\'strict\'" />
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147 <param label="--p-feat-ext--encoding: TEXT [default: \'utf-8\']" name="pfeatextencoding" optional="False" type="text" value="\'utf-8\'" />
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148 <param label="--p-feat-ext--input: TEXT [default: \'content\']" name="pfeatextinput" optional="False" type="text" value="\'content\'" />
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149 <param label="--p-no-feat-ext--lowercase: Do not [default: True]" name="pnofeatextlowercase" selected="False" type="boolean" />
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150 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192" />
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151 <param label="--p-feat-ext--ngram-range: TEXT [default: \'[7, 7]\']" name="pfeatextngramrange" optional="False" type="text" value="\'[7, 7]" />
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152 <param label="--p-feat-ext--norm: TEXT [default: \'l2\']" name="pfeatextnorm" optional="False" type="text" value="\'l2\'" />
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153 <param label="--p-feat-ext--preprocessor: TEXT [default: \'null\']" name="pfeatextpreprocessor" optional="False" type="text" value="\'null\'" />
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154 <param label="--p-feat-ext--stop-words: TEXT [default: \'null\']" name="pfeatextstopwords" optional="False" type="text" value="\'null\'" />
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155 <param label="--p-feat-ext--strip-accents: TEXT [default: \'null\']" name="pfeatextstripaccents" optional="False" type="text" value="\'null\'" />
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156 <param label="--p-feat-ext--token-pattern: TEXT [default: \'(?u)\\\\b\\\\w\\\\w+\\\\b\']" name="pfeatexttokenpattern" optional="False" type="text" value="\'(?u)\\\\b\\\\w\\\\w+\\\\b\'" />
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157 <param label="--p-feat-ext--tokenizer: TEXT [default: \'null\']" name="pfeatexttokenizer" optional="False" type="text" value="\'null\'" />
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158 <param label="--p-verbose: --p-verbose: / --p-no-verbose [default: False]" name="pverbose" selected="False" type="boolean" />
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159 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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160
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161 </inputs>
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162
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163 <outputs>
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164 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier" />
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165
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166 </outputs>
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167
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168 <help><![CDATA[
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169 Train the naive_bayes classifier
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170 ###############################################################
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171
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172 Create a scikit-learn naive_bayes classifier for reads
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173
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174 Parameters
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175 ----------
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176 reference_reads : FeatureData[Sequence]
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177 reference_taxonomy : FeatureData[Taxonomy]
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178 class_weight : FeatureTable[RelativeFrequency], optional
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179 classify__alpha : Float, optional
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180 classify__chunk_size : Int, optional
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181 classify__class_prior : Str, optional
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182 classify__fit_prior : Bool, optional
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183 feat_ext__alternate_sign : Bool, optional
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184 feat_ext__analyzer : Str, optional
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185 feat_ext__binary : Bool, optional
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186 feat_ext__decode_error : Str, optional
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187 feat_ext__encoding : Str, optional
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188 feat_ext__input : Str, optional
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189 feat_ext__lowercase : Bool, optional
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190 feat_ext__n_features : Int, optional
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191 feat_ext__ngram_range : Str, optional
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192 feat_ext__norm : Str, optional
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193 feat_ext__preprocessor : Str, optional
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194 feat_ext__stop_words : Str, optional
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195 feat_ext__strip_accents : Str, optional
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196 feat_ext__token_pattern : Str, optional
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197 feat_ext__tokenizer : Str, optional
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198 verbose : Bool, optional
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199
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200 Returns
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201 -------
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202 classifier : TaxonomicClassifier
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203 ]]></help>
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204 <macros>
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205 <import>qiime_citation.xml</import>
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206 </macros>
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207 <expand macro="qiime_citation"/>
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208 </tool> |
