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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 #if str($pclassifyclassprior):
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35 --p-classify--class-prior="$pclassifyclassprior"
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36 #end if
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37
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38 #if $pclassifyfitprior:
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39 --p-classify--fit-prior
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40 #end if
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41
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42 #if $pfeatextalternatesign:
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43 --p-feat-ext--alternate-sign
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44 #end if
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45
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46 #if str($pfeatextanalyzer):
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47 --p-feat-ext--analyzer="$pfeatextanalyzer"
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48 #end if
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49
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50 #if $pfeatextbinary:
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51 --p-feat-ext--binary
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52 #end if
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53
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54 #if str($pfeatextdecodeerror):
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55 --p-feat-ext--decode-error="$pfeatextdecodeerror"
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56 #end if
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57
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58 #if str($pfeatextencoding):
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59 --p-feat-ext--encoding="$pfeatextencoding"
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60 #end if
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61
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62 #if str($pfeatextinput):
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63 --p-feat-ext--input="$pfeatextinput"
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64 #end if
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65
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66 #if $pnofeatextlowercase:
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67 --p-no-feat-ext--lowercase
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68 #end if
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69
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70 #if $pfeatextnfeatures:
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71 --p-feat-ext--n-features=$pfeatextnfeatures
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72 #end if
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73
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74 #if '__ob__' in str($pfeatextngramrange):
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75 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
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76 #set $pfeatextngramrange = $pfeatextngramrange_temp
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77 #end if
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78 #if 'X' in str($pfeatextngramrange):
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79 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
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80 #set $pfeatextngramrange = $pfeatextngramrange_temp
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81 #end if
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82
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83 #if str($pfeatextngramrange):
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84 --p-feat-ext--ngram-range="$pfeatextngramrange"
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85 #end if
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86
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87
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88 #if $pfeatextnonnegative:
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89 --p-feat-ext--non-negative
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90 #end if
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91
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92 #if str($pfeatextnorm):
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93 --p-feat-ext--norm="$pfeatextnorm"
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94 #end if
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95
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96 #if str($pfeatextpreprocessor):
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97 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
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98 #end if
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99
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100 #if str($pfeatextstopwords):
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101 --p-feat-ext--stop-words="$pfeatextstopwords"
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102 #end if
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103
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104 #if str($pfeatextstripaccents):
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105 --p-feat-ext--strip-accents="$pfeatextstripaccents"
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106 #end if
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107
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108 #if '__ob__' in str($pfeatexttokenpattern):
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109 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
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110 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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111 #end if
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112 #if 'X' in str($pfeatexttokenpattern):
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113 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
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114 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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115 #end if
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116
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117 #if str($pfeatexttokenpattern):
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118 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
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119 #end if
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120
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121
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122 #if str($pfeatexttokenizer):
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123 --p-feat-ext--tokenizer="$pfeatexttokenizer"
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124 #end if
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125
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126 --o-classifier=oclassifier
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127 ;
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128 cp oclassifier.qza $oclassifier
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129 ]]></command>
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130 <inputs>
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131 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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132 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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133
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134 <conditional name="id_to_taxonomy_fp" optional="True">
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135 <param name="selector" type="select" label="Reference taxonomy to query">
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136 <option value="cached">Public databases</option>
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137 <option value="history">Databases from your history</option>
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138 </param>
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139 <when value="cached">
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140 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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141 <options from_data_table="qiime_taxonomy" />
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142 </param>
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143 </when>
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144 <when value="history">
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145 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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146 </when>
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147 </conditional>
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148
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149 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
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150 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
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151 <param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="'null'"/>
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152 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
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153 <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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154 <param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="'char_wb'"/>
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155 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
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156 <param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="'strict'"/>
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157 <param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="'utf-8'"/>
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158 <param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="'content'"/>
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159 <param label="--p-no-feat-ext--lowercase: [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
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160 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
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161 <param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="'[7, 7]"/>
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162 <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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163 <param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="'l2'"/>
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164 <param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="'null'"/>
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165 <param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="'null'"/>
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166 <param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="'null'"/>
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167 <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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168 <param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="'null'"/>
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169 </inputs>
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170 <outputs>
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171 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
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172 </outputs>
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173 <help><![CDATA[
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174 Train the naive_bayes classifier
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175 ################################
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176
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177 Create a scikit-learn naive_bayes classifier for reads
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178
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179 Parameters
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180 ----------
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181 reference_reads : FeatureData[Sequence]
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182 \
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183
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184 reference_taxonomy : FeatureData[Taxonomy]
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185 \
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186
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187 class_weight : FeatureTable[RelativeFrequency], optional
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188 \
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189
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190 classify__alpha : Float, optional
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191 \
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192
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193 classify__chunk_size : Int, optional
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194 \
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195
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196 classify__class_prior : Str, optional
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197 \
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198
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199 classify__fit_prior : Bool, optional
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200 \
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201
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202 feat_ext__alternate_sign : Bool, optional
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203 \
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204
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205 feat_ext__analyzer : Str, optional
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206 \
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207
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208 feat_ext__binary : Bool, optional
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209 \
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210
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211 feat_ext__decode_error : Str, optional
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212 \
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213
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214 feat_ext__encoding : Str, optional
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215 \
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216
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217 feat_ext__input : Str, optional
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218 \
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219
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220 feat_ext__lowercase : Bool, optional
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221 \
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222
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223 feat_ext__n_features : Int, optional
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224 \
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225
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226 feat_ext__ngram_range : Str, optional
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227 \
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228
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229 feat_ext__non_negative : Bool, optional
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230 \
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231
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232 feat_ext__norm : Str, optional
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233 \
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234
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235 feat_ext__preprocessor : Str, optional
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236 \
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237
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238 feat_ext__stop_words : Str, optional
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239 \
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240
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241 feat_ext__strip_accents : Str, optional
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242 \
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243
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244 feat_ext__token_pattern : Str, optional
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245 \
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246
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247 feat_ext__tokenizer : Str, optional
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248 \
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249
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250 Returns
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251 -------
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252 classifier : TaxonomicClassifier
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253 \
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254
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255 ]]></help>
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256 <macros>
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257 <import>qiime_citation.xml</import>
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258 </macros>
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259 <expand macro="qiime_citation"/>
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260 </tool>
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