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comparison qiime2-2020.8/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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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>