Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 20:d93d8888f0b0 draft
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| author | florianbegusch |
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| date | Fri, 04 Sep 2020 12:44:24 +0000 |
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| 19:6c48f8d82424 | 20:d93d8888f0b0 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_feature-classifier_fit-classifier-naive-bayes" name="qiime feature-classifier fit-classifier-naive-bayes" | |
| 3 version="2020.8"> | |
| 4 <description>Train the naive_bayes classifier</description> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="2020.8">qiime2</requirement> | |
| 7 </requirements> | |
| 8 <command><![CDATA[ | |
| 9 qiime feature-classifier fit-classifier-naive-bayes | |
| 10 | |
| 11 --i-reference-reads=$ireferencereads | |
| 12 | |
| 13 --i-reference-taxonomy=$ireferencetaxonomy | |
| 14 | |
| 15 #if str($iclassweight) != 'None': | |
| 16 --i-class-weight=$iclassweight | |
| 17 #end if | |
| 18 | |
| 19 --p-classify--alpha=$pclassifyalpha | |
| 20 | |
| 21 --p-classify--chunk-size=$pclassifychunksize | |
| 22 | |
| 23 #if str($pclassifyclassprior): | |
| 24 --p-classify--class-prior=$pclassifyclassprior | |
| 25 #end if | |
| 26 #if $pclassifyfitprior: | |
| 27 --p-classify--fit-prior | |
| 28 #end if | |
| 29 | |
| 30 #if $pfeatextalternatesign: | |
| 31 --p-feat-ext--alternate-sign | |
| 32 #end if | |
| 33 | |
| 34 #if str($pfeatextanalyzer): | |
| 35 --p-feat-ext--analyzer=$pfeatextanalyzer | |
| 36 #end if | |
| 37 #if $pfeatextbinary: | |
| 38 --p-feat-ext--binary | |
| 39 #end if | |
| 40 | |
| 41 #if str($pfeatextdecodeerror): | |
| 42 --p-feat-ext--decode-error=$pfeatextdecodeerror | |
| 43 #end if | |
| 44 #if str($pfeatextencoding): | |
| 45 --p-feat-ext--encoding=$pfeatextencoding | |
| 46 #end if | |
| 47 #if str($pfeatextinput): | |
| 48 --p-feat-ext--input=$pfeatextinput | |
| 49 #end if | |
| 50 #if $pnofeatextlowercase: | |
| 51 --p-no-feat-ext--lowercase | |
| 52 #end if | |
| 53 | |
| 54 --p-feat-ext--n-features=$pfeatextnfeatures | |
| 55 | |
| 56 #if '__ob__' in str($pfeatextngramrange): | |
| 57 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[') | |
| 58 #set $pfeatextngramrange = $pfeatextngramrange_temp | |
| 59 #end if | |
| 60 #if '__cb__' in str($pfeatextngramrange): | |
| 61 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__cb__', ']') | |
| 62 #set $pfeatextngramrange = $pfeatextngramrange_temp | |
| 63 #end if | |
| 64 #if 'X' in str($pfeatextngramrange): | |
| 65 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\') | |
| 66 #set $pfeatextngramrange = $pfeatextngramrange_temp | |
| 67 #end if | |
| 68 #if '__sq__' in str($pfeatextngramrange): | |
| 69 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'") | |
| 70 #set $pfeatextngramrange = $pfeatextngramrange_temp | |
| 71 #end if | |
| 72 #if '__db__' in str($pfeatextngramrange): | |
| 73 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__db__', '"') | |
| 74 #set $pfeatextngramrange = $pfeatextngramrange_temp | |
| 75 #end if | |
| 76 | |
| 77 #if str($pfeatextngramrange): | |
| 78 --p-feat-ext--ngram-range=$pfeatextngramrange | |
| 79 #end if | |
| 80 | |
| 81 #if str($pfeatextnorm): | |
| 82 --p-feat-ext--norm=$pfeatextnorm | |
| 83 #end if | |
| 84 #if str($pfeatextpreprocessor): | |
| 85 --p-feat-ext--preprocessor=$pfeatextpreprocessor | |
| 86 #end if | |
| 87 #if str($pfeatextstopwords): | |
| 88 --p-feat-ext--stop-words=$pfeatextstopwords | |
| 89 #end if | |
| 90 #if str($pfeatextstripaccents): | |
| 91 --p-feat-ext--strip-accents=$pfeatextstripaccents | |
| 92 #end if | |
| 93 #if '__ob__' in str($pfeatexttokenpattern): | |
| 94 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[') | |
| 95 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp | |
| 96 #end if | |
| 97 #if '__cb__' in str($pfeatexttokenpattern): | |
| 98 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__cb__', ']') | |
| 99 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp | |
| 100 #end if | |
| 101 #if 'X' in str($pfeatexttokenpattern): | |
| 102 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\') | |
| 103 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp | |
| 104 #end if | |
| 105 #if '__sq__' in str($pfeatexttokenpattern): | |
| 106 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'") | |
| 107 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp | |
| 108 #end if | |
| 109 #if '__db__' in str($pfeatexttokenpattern): | |
| 110 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__db__', '"') | |
| 111 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp | |
| 112 #end if | |
| 113 | |
| 114 #if str($pfeatexttokenpattern): | |
| 115 --p-feat-ext--token-pattern=$pfeatexttokenpattern | |
| 116 #end if | |
| 117 | |
| 118 #if str($pfeatexttokenizer): | |
| 119 --p-feat-ext--tokenizer=$pfeatexttokenizer | |
| 120 #end if | |
| 121 #if $pverbose: | |
| 122 --p-verbose | |
| 123 #end if | |
| 124 | |
| 125 --o-classifier=oclassifier | |
| 126 | |
| 127 #if str($examples) != 'None': | |
| 128 --examples=$examples | |
| 129 #end if | |
| 130 | |
| 131 ; | |
| 132 cp oclassifier.qza $oclassifier | |
| 133 | |
| 134 ]]></command> | |
| 135 <inputs> | |
| 136 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data" /> | |
| 137 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" /> | |
| 138 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" /> | |
| 139 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001" /> | |
| 140 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000" /> | |
| 141 <param label="--p-classify--class-prior: TEXT [default: \'null\']" name="pclassifyclassprior" optional="False" type="text" value="\'null\'" /> | |
| 142 <param label="--p-classify--fit-prior: --p-classify--fit-prior: / --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean" /> | |
| 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" /> | |
| 144 <param label="--p-feat-ext--analyzer: TEXT [default: \'char_wb\']" name="pfeatextanalyzer" optional="False" type="text" value="\'char_wb\'" /> | |
| 145 <param label="--p-feat-ext--binary: --p-feat-ext--binary: / --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean" /> | |
| 146 <param label="--p-feat-ext--decode-error: TEXT [default: \'strict\']" name="pfeatextdecodeerror" optional="False" type="text" value="\'strict\'" /> | |
| 147 <param label="--p-feat-ext--encoding: TEXT [default: \'utf-8\']" name="pfeatextencoding" optional="False" type="text" value="\'utf-8\'" /> | |
| 148 <param label="--p-feat-ext--input: TEXT [default: \'content\']" name="pfeatextinput" optional="False" type="text" value="\'content\'" /> | |
| 149 <param label="--p-no-feat-ext--lowercase: Do not [default: True]" name="pnofeatextlowercase" selected="False" type="boolean" /> | |
| 150 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192" /> | |
| 151 <param label="--p-feat-ext--ngram-range: TEXT [default: \'[7, 7]\']" name="pfeatextngramrange" optional="False" type="text" value="\'[7, 7]" /> | |
| 152 <param label="--p-feat-ext--norm: TEXT [default: \'l2\']" name="pfeatextnorm" optional="False" type="text" value="\'l2\'" /> | |
| 153 <param label="--p-feat-ext--preprocessor: TEXT [default: \'null\']" name="pfeatextpreprocessor" optional="False" type="text" value="\'null\'" /> | |
| 154 <param label="--p-feat-ext--stop-words: TEXT [default: \'null\']" name="pfeatextstopwords" optional="False" type="text" value="\'null\'" /> | |
| 155 <param label="--p-feat-ext--strip-accents: TEXT [default: \'null\']" name="pfeatextstripaccents" optional="False" type="text" value="\'null\'" /> | |
| 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\'" /> | |
| 157 <param label="--p-feat-ext--tokenizer: TEXT [default: \'null\']" name="pfeatexttokenizer" optional="False" type="text" value="\'null\'" /> | |
| 158 <param label="--p-verbose: --p-verbose: / --p-no-verbose [default: False]" name="pverbose" selected="False" type="boolean" /> | |
| 159 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
| 160 | |
| 161 </inputs> | |
| 162 | |
| 163 <outputs> | |
| 164 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier" /> | |
| 165 | |
| 166 </outputs> | |
| 167 | |
| 168 <help><![CDATA[ | |
| 169 Train the naive_bayes classifier | |
| 170 ############################################################### | |
| 171 | |
| 172 Create a scikit-learn naive_bayes classifier for reads | |
| 173 | |
| 174 Parameters | |
| 175 ---------- | |
| 176 reference_reads : FeatureData[Sequence] | |
| 177 reference_taxonomy : FeatureData[Taxonomy] | |
| 178 class_weight : FeatureTable[RelativeFrequency], optional | |
| 179 classify__alpha : Float, optional | |
| 180 classify__chunk_size : Int, optional | |
| 181 classify__class_prior : Str, optional | |
| 182 classify__fit_prior : Bool, optional | |
| 183 feat_ext__alternate_sign : Bool, optional | |
| 184 feat_ext__analyzer : Str, optional | |
| 185 feat_ext__binary : Bool, optional | |
| 186 feat_ext__decode_error : Str, optional | |
| 187 feat_ext__encoding : Str, optional | |
| 188 feat_ext__input : Str, optional | |
| 189 feat_ext__lowercase : Bool, optional | |
| 190 feat_ext__n_features : Int, optional | |
| 191 feat_ext__ngram_range : Str, optional | |
| 192 feat_ext__norm : Str, optional | |
| 193 feat_ext__preprocessor : Str, optional | |
| 194 feat_ext__stop_words : Str, optional | |
| 195 feat_ext__strip_accents : Str, optional | |
| 196 feat_ext__token_pattern : Str, optional | |
| 197 feat_ext__tokenizer : Str, optional | |
| 198 verbose : Bool, optional | |
| 199 | |
| 200 Returns | |
| 201 ------- | |
| 202 classifier : TaxonomicClassifier | |
| 203 ]]></help> | |
| 204 <macros> | |
| 205 <import>qiime_citation.xml</import> | |
| 206 </macros> | |
| 207 <expand macro="qiime_citation"/> | |
| 208 </tool> |