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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime feature-classifier fit-classifier-naive-bayes
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10
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11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
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12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
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13 --i-reference-taxonomy '$tax'
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14 #else:
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15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
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16 --i-reference-taxonomy '$tax'
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17 #end if
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18
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19
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20 --i-reference-reads=$ireferencereads
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21
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22 #if $pfeatextnonnegative:
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23 --p-feat-ext--non-negative
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24 #else
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25 --p-no-feat-ext--non-negative
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26 #end if
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27
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28 #if str($pfeatexttokenpattern):
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29 #if '__ob__' in str($pfeatexttokenpattern):
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30 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
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31 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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32 #end if
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33 #if 'X' in str($pfeatexttokenpattern):
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34 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
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35 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
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36 #end if
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37 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
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38 #end if
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39
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40 #if str($pfeatextencoding):
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41 --p-feat-ext--encoding="$pfeatextencoding"
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42 #end if
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43
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44 #if $pfeatextnfeatures:
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45 --p-feat-ext--n-features=$pfeatextnfeatures
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46 #end if
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47
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48 #if str($pfeatextstopwords):
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49 --p-feat-ext--stop-words="$pfeatextstopwords"
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50 #end if
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51
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52 #if str($pfeatextngramrange):
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53 #if '__ob__' in str($pfeatextngramrange):
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54 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
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55 #set $pfeatextngramrange = $pfeatextngramrange_temp
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56 #end if
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57 #if 'X' in str($pfeatextngramrange):
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58 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
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59 #set $pfeatextngramrange = $pfeatextngramrange_temp
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60 #end if
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61 --p-feat-ext--ngram-range="$pfeatextngramrange"
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62 #end if
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63
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64 #if str($pfeatextanalyzer):
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65 --p-feat-ext--analyzer="$pfeatextanalyzer"
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66 #end if
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67
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68 #if $pclassifyalpha:
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69 --p-classify--alpha=$pclassifyalpha
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70 #end if
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71
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72 #if str($cmdconfig) != 'None':
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73 --cmd-config=$cmdconfig
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74 #end if
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75
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76 #if $pclassifyfitprior:
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77 --p-classify--fit-prior
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78 #else
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79 --p-no-classify--fit-prior
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80 #end if
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81
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82 #if $pfeatextbinary:
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83 --p-feat-ext--binary
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84 #else
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85 --p-no-feat-ext--binary
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86 #end if
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87
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88 #if str($iclassweight) != 'None':
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89 --i-class-weight=$iclassweight
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90 #end if
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91
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92 #if str($pfeatextpreprocessor):
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93 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
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94 #end if
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95
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96 #if $pfeatextalternatesign:
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97 --p-feat-ext--alternate-sign
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98 #else
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99 --p-no-feat-ext--alternate-sign
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100 #end if
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101
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102 #if $pclassifychunksize:
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103 --p-classify--chunk-size=$pclassifychunksize
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104 #end if
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105
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106 #if str($pclassifyclassprior):
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107 --p-classify--class-prior="$pclassifyclassprior"
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108 #end if
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109
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110 #if str($pmemory):
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111 --p-memory="$pmemory"
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112 #end if
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113
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114 #if $pfeatextlowercase:
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115 --p-feat-ext--lowercase
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116 #else
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117 --p-no-feat-ext--lowercase
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118 #end if
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119
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120 #if str($pfeatextinput):
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121 --p-feat-ext--input="$pfeatextinput"
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122 #end if
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123
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124 #if str($pfeatexttokenizer):
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125 --p-feat-ext--tokenizer="$pfeatexttokenizer"
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126 #end if
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127 --o-classifier=oclassifier
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128 #if str($pfeatextnorm):
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129 --p-feat-ext--norm="$pfeatextnorm"
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130 #end if
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131
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132 #if str($pfeatextdecodeerror):
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133 --p-feat-ext--decode-error="$pfeatextdecodeerror"
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134 #end if
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135
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136 #if str($pfeatextstripaccents):
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137 --p-feat-ext--strip-accents="$pfeatextstripaccents"
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138 #end if
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139 ;
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140 cp oclassifier.qza $oclassifier;
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141 ]]>
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142 </command>
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143 <inputs>
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144 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
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145
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146 <conditional name="id_to_taxonomy_fp" optional="True">
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147 <param name="selector" type="select" label="Reference taxonomy to query">
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148 <option value="cached">Public databases</option>
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149 <option value="history">Databases from your history</option>
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150 </param>
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151 <when value="cached">
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152 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
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153 <options from_data_table="qiime_taxonomy" />
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154 </param>
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155 </when>
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156 <when value="history">
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157 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
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158 </when>
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159 </conditional>
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160
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161 <param format="qza,no_unzip.zip" label="--i-class-weight: FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
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162
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163 <param label="--p-classify--alpha: [default: 0.01]" name="pclassifyalpha" optional="True" type="float" value="0.01"/>
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164 <param label="--p-classify--chunk-size: [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
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165
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166 <param label="--p-classify--class-prior: [default: null]" name="pclassifyclassprior" optional="True" type="text" value="null"/>
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167 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" checked="False" type="boolean"/>
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168
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169 <param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" checked="False" type="boolean"/>
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170
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171 <param label="--p-feat-ext--analyzer: [default: char_wb]" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
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172 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" checked="False" type="boolean"/>
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173
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174 <param label="--p-feat-ext--decode-error: [default: strict]" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
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175
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176 <param label="--p-feat-ext--encoding: [default: utf-8]" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
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177 <param label="--p-feat-ext--input: [default: content]" name="pfeatextinput" optional="True" type="text" value="content"/>
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178 <param label="--p-feat-ext--lowercase: --p-no-feat-ext--lowercase [default: True]" name="pfeatextlowercase" checked="True" type="boolean"/>
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179
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180 <param label="--p-feat-ext--n-features: [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
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181
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182 <param label="--p-feat-ext--ngram-range: [default: [8, 8]]" name="pfeatextngramrange" optional="True" type="text" value="[8, 8]"/>
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183 <param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" checked="False" type="boolean"/>
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184
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185 <param label="--p-feat-ext--norm: [default: l2]" name="pfeatextnorm" optional="True" type="text" value="l2"/>
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186 <param label="--p-feat-ext--preprocessor: [default: null]" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
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187
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188 <param label="--p-feat-ext--stop-words: [default: null]" name="pfeatextstopwords" optional="True" type="text" value="null"/>
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189 <param label="--p-feat-ext--strip-accents: [default: null]" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
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190
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191 <param label="--p-feat-ext--token-pattern: [default: (?u)\b\w\w+\b]" name="pfeatexttokenpattern" optional="True" type="text" value="(?u)\b\w\w+\b"/>
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192
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193 <param label="--p-feat-ext--tokenizer: [default: null]" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
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194
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195 <param label="--p-memory: [default: null]" name="pmemory" optional="True" type="text" value="null"/>
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196
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197 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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198 </inputs>
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199 <outputs>
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200 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
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201 </outputs>
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202 <help>
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203 <![CDATA[
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204 Train the naive_bayes classifier
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205 --------------------------------
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206
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207 Create a scikit-learn naive_bayes classifier for reads
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208
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209 Parameters
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210 ----------
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211 reference_reads : FeatureData[Sequence]
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212 \
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213 reference_taxonomy : FeatureData[Taxonomy]
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214 \
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215 class_weight : FeatureTable[RelativeFrequency], optional
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216 \
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217 classify__alpha : Float, optional
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218 \
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219 classify__chunk_size : Int, optional
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220 \
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221 classify__class_prior : Str, optional
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222 \
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223 classify__fit_prior : Bool, optional
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224 \
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225 feat_ext__alternate_sign : Bool, optional
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226 \
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227 feat_ext__analyzer : Str, optional
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228 \
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229 feat_ext__binary : Bool, optional
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230 \
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231 feat_ext__decode_error : Str, optional
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232 \
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233 feat_ext__encoding : Str, optional
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234 \
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235 feat_ext__input : Str, optional
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236 \
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237 feat_ext__lowercase : Bool, optional
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238 \
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239 feat_ext__n_features : Int, optional
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240 \
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241 feat_ext__ngram_range : Str, optional
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242 \
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243 feat_ext__non_negative : Bool, optional
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244 \
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245 feat_ext__norm : Str, optional
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246 \
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247 feat_ext__preprocessor : Str, optional
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248 \
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249 feat_ext__stop_words : Str, optional
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250 \
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251 feat_ext__strip_accents : Str, optional
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252 \
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253 feat_ext__token_pattern : Str, optional
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254 \
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255 feat_ext__tokenizer : Str, optional
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256 \
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257 memory : Str, optional
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258 \
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259
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260 Returns
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261 -------
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262 classifier : TaxonomicClassifier
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263 \
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264 ]]>
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265 </help>
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266 </tool>
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