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comparison qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
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3:eda5df31da55 4:71f124e02000
3 <description> - Train the naive_bayes classifier</description> 3 <description> - Train the naive_bayes classifier</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime feature-classifier fit-classifier-naive-bayes
9
10 --i-reference-reads=$ireferencereads
11 8
12 9
13 #if str( $id_to_taxonomy_fp.selector ) == 'history' 10 #if str( $id_to_taxonomy_fp.selector ) == 'history'
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp 11 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
15 --i-reference-taxonomy '$tax'
16 #else: 12 #else:
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path 13 #set $tax_path = $id_to_taxonomy_fp.taxonomy_fp.fields.path
18 --i-reference-taxonomy '$tax' 14 qiime tools import --type 'FeatureData[Taxonomy]' --source-format HeaderlessTSVTaxonomyFormat --input-path $tax_path --output-path ref-taxonomy.qza;
19 #end if 15 #set $tax='ref-taxonomy.qza'
20 16 #end if
17
18
19 qiime feature-classifier fit-classifier-naive-bayes
20
21
22 --i-reference-taxonomy '$tax'
23
24
25 --i-reference-reads=$ireferencereads
21 26
22 #if str($iclassweight) != 'None': 27 #if str($iclassweight) != 'None':
23 --i-class-weight=$iclassweight 28 --i-class-weight=$iclassweight
24 #end if 29 #end if
25 30
26 #if $pclassifyalpha: 31 #if str($pclassifyalpha):
27 --p-classify--alpha=$pclassifyalpha 32 --p-classify--alpha=$pclassifyalpha
28 #end if 33 #end if
29 34
30 #if $pclassifychunksize: 35 #if str($pclassifychunksize):
31 --p-classify--chunk-size=$pclassifychunksize 36 --p-classify--chunk-size=$pclassifychunksize
37 #end if
38
39
40
41
42 #if '__sq__' in str($pclassifyclassprior):
43 #set $pclassifyclassprior_temp = $pclassifyclassprior.replace('__sq__', "'")
44 #set $pclassifyclassprior = $pclassifyclassprior_temp
32 #end if 45 #end if
33 46
34 #if str($pclassifyclassprior): 47 #if str($pclassifyclassprior):
35 --p-classify--class-prior="$pclassifyclassprior" 48 --p-classify--class-prior="$pclassifyclassprior"
36 #end if 49 #end if
37 50
51
52
53
38 #if $pclassifyfitprior: 54 #if $pclassifyfitprior:
39 --p-classify--fit-prior 55 --p-classify--fit-prior
40 #end if 56 #end if
41 57
42 #if $pfeatextalternatesign: 58 #if $pfeatextalternatesign:
43 --p-feat-ext--alternate-sign 59 --p-feat-ext--alternate-sign
44 #end if 60 #end if
45 61
62
63
64
65
66 #if '__sq__' in str($pfeatextanalyzer):
67 #set $pfeatextanalyzer_temp = $pfeatextanalyzer.replace('__sq__', "'")
68 #set $pfeatextanalyzer = $pfeatextanalyzer_temp
69 #end if
70
46 #if str($pfeatextanalyzer): 71 #if str($pfeatextanalyzer):
47 --p-feat-ext--analyzer="$pfeatextanalyzer" 72 --p-feat-ext--analyzer="$pfeatextanalyzer"
48 #end if 73 #end if
49 74
75
76
77
78
50 #if $pfeatextbinary: 79 #if $pfeatextbinary:
51 --p-feat-ext--binary 80 --p-feat-ext--binary
52 #end if 81 #end if
53 82
83
84
85 #if '__sq__' in str($pfeatextdecodeerror):
86 #set $pfeatextdecodeerror_temp = $pfeatextdecodeerror.replace('__sq__', "'")
87 #set $pfeatextdecodeerror = $pfeatextdecodeerror_temp
88 #end if
89
54 #if str($pfeatextdecodeerror): 90 #if str($pfeatextdecodeerror):
55 --p-feat-ext--decode-error="$pfeatextdecodeerror" 91 --p-feat-ext--decode-error="$pfeatextdecodeerror"
56 #end if 92 #end if
57 93
94
95
96
97
98 #if '__sq__' in str($pfeatextencoding):
99 #set $pfeatextencoding_temp = $pfeatextencoding.replace('__sq__', "'")
100 #set $pfeatextencoding = $pfeatextencoding_temp
101 #end if
102
58 #if str($pfeatextencoding): 103 #if str($pfeatextencoding):
59 --p-feat-ext--encoding="$pfeatextencoding" 104 --p-feat-ext--encoding="$pfeatextencoding"
60 #end if 105 #end if
61 106
107
108
109
110
111 #if '__sq__' in str($pfeatextinput):
112 #set $pfeatextinput_temp = $pfeatextinput.replace('__sq__', "'")
113 #set $pfeatextinput = $pfeatextinput_temp
114 #end if
115
62 #if str($pfeatextinput): 116 #if str($pfeatextinput):
63 --p-feat-ext--input="$pfeatextinput" 117 --p-feat-ext--input="$pfeatextinput"
64 #end if 118 #end if
65 119
120
121
122
66 #if $pnofeatextlowercase: 123 #if $pnofeatextlowercase:
67 --p-no-feat-ext--lowercase 124 --p-no-feat-ext--lowercase
68 #end if 125 #end if
69 126
70 #if $pfeatextnfeatures: 127 #if str($pfeatextnfeatures):
71 --p-feat-ext--n-features=$pfeatextnfeatures 128 --p-feat-ext--n-features=$pfeatextnfeatures
129 #end if
130
131
132
133
134 #if '__sq__' in str($pfeatextngramrange):
135 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__sq__', "'")
136 #set $pfeatextngramrange = $pfeatextngramrange_temp
72 #end if 137 #end if
73 138
74 #if '__ob__' in str($pfeatextngramrange): 139 #if '__ob__' in str($pfeatextngramrange):
75 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[') 140 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
76 #set $pfeatextngramrange = $pfeatextngramrange_temp 141 #set $pfeatextngramrange = $pfeatextngramrange_temp
83 #if str($pfeatextngramrange): 148 #if str($pfeatextngramrange):
84 --p-feat-ext--ngram-range="$pfeatextngramrange" 149 --p-feat-ext--ngram-range="$pfeatextngramrange"
85 #end if 150 #end if
86 151
87 152
153
154
155
88 #if $pfeatextnonnegative: 156 #if $pfeatextnonnegative:
89 --p-feat-ext--non-negative 157 --p-feat-ext--non-negative
90 #end if 158 #end if
91 159
160
161 #if '__sq__' in str($pfeatextnorm):
162 #set $pfeatextnorm_temp = $pfeatextnorm.replace('__sq__', "'")
163 #set $pfeatextnorm = $pfeatextnorm_temp
164 #end if
165
92 #if str($pfeatextnorm): 166 #if str($pfeatextnorm):
93 --p-feat-ext--norm="$pfeatextnorm" 167 --p-feat-ext--norm="$pfeatextnorm"
94 #end if 168 #end if
95 169
170
171
172
173 #if '__sq__' in str($pfeatextpreprocessor):
174 #set $pfeatextpreprocessor_temp = $pfeatextpreprocessor.replace('__sq__', "'")
175 #set $pfeatextpreprocessor = $pfeatextpreprocessor_temp
176 #end if
177
96 #if str($pfeatextpreprocessor): 178 #if str($pfeatextpreprocessor):
97 --p-feat-ext--preprocessor="$pfeatextpreprocessor" 179 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
98 #end if 180 #end if
99 181
182
183
184
185 #if '__sq__' in str($pfeatextstopwords):
186 #set $pfeatextstopwords_temp = $pfeatextstopwords.replace('__sq__', "'")
187 #set $pfeatextstopwords = $pfeatextstopwords_temp
188 #end if
189
100 #if str($pfeatextstopwords): 190 #if str($pfeatextstopwords):
101 --p-feat-ext--stop-words="$pfeatextstopwords" 191 --p-feat-ext--stop-words="$pfeatextstopwords"
102 #end if 192 #end if
103 193
194
195
196
197
198 #if '__sq__' in str($pfeatextstripaccents):
199 #set $pfeatextstripaccents_temp = $pfeatextstripaccents.replace('__sq__', "'")
200 #set $pfeatextstripaccents = $pfeatextstripaccents_temp
201 #end if
202
104 #if str($pfeatextstripaccents): 203 #if str($pfeatextstripaccents):
105 --p-feat-ext--strip-accents="$pfeatextstripaccents" 204 --p-feat-ext--strip-accents="$pfeatextstripaccents"
205 #end if
206
207
208
209
210
211
212 #if '__sq__' in str($pfeatexttokenpattern):
213 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__sq__', "'")
214 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
106 #end if 215 #end if
107 216
108 #if '__ob__' in str($pfeatexttokenpattern): 217 #if '__ob__' in str($pfeatexttokenpattern):
109 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[') 218 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
110 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp 219 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
111 #end if 220 #end if
221
112 #if 'X' in str($pfeatexttokenpattern): 222 #if 'X' in str($pfeatexttokenpattern):
113 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\') 223 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
114 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp 224 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
115 #end if 225 #end if
116 226
117 #if str($pfeatexttokenpattern): 227 #if str($pfeatexttokenpattern):
118 --p-feat-ext--token-pattern="$pfeatexttokenpattern" 228 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
119 #end if 229 #end if
120 230
231
232
233
234
235 #if '__sq__' in str($pfeatexttokenizer):
236 #set $pfeatexttokenizer_temp = $pfeatexttokenizer.replace('__sq__', "'")
237 #set $pfeatexttokenizer = $pfeatexttokenizer_temp
238 #end if
121 239
122 #if str($pfeatexttokenizer): 240 #if str($pfeatexttokenizer):
123 --p-feat-ext--tokenizer="$pfeatexttokenizer" 241 --p-feat-ext--tokenizer="$pfeatexttokenizer"
124 #end if 242 #end if
125 243
146 </when> 264 </when>
147 </conditional> 265 </conditional>
148 266
149 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/> 267 <param label="--p-classify--alpha: NUMBER [default: 0.001]" name="pclassifyalpha" optional="True" type="float" value="0.001"/>
150 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/> 268 <param label="--p-classify--chunk-size: INTEGER [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
151 <param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="'null'"/> 269 <param label="--p-classify--class-prior: TEXT [default: 'null']" name="pclassifyclassprior" optional="True" type="text" value="null"/>
152 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/> 270 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" selected="False" type="boolean"/>
153 <param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean"/> 271 <param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" selected="False" type="boolean"/>
154 <param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="'char_wb'"/> 272 <param label="--p-feat-ext--analyzer: TEXT [default: 'char_wb']" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
155 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/> 273 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" selected="False" type="boolean"/>
156 <param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="'strict'"/> 274 <param label="--p-feat-ext--decode-error: TEXT [default: 'strict']" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
157 <param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="'utf-8'"/> 275 <param label="--p-feat-ext--encoding: TEXT [default: 'utf-8']" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
158 <param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="'content'"/> 276 <param label="--p-feat-ext--input: TEXT [default: 'content']" name="pfeatextinput" optional="True" type="text" value="content"/>
159 <param label="--p-no-feat-ext--lowercase: [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/> 277 <param label="--p-no-feat-ext--lowercase: [default: False]" name="pnofeatextlowercase" selected="False" type="boolean"/>
160 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/> 278 <param label="--p-feat-ext--n-features: INTEGER [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
161 <param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="'[7, 7]"/> 279 <param label="--p-feat-ext--ngram-range: TEXT [default: '[7, 7]']" name="pfeatextngramrange" optional="True" type="text" value="[7, 7]"/>
162 <param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" selected="False" type="boolean"/> 280 <param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" selected="False" type="boolean"/>
163 <param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="'l2'"/> 281 <param label="--p-feat-ext--norm: TEXT [default: 'l2']" name="pfeatextnorm" optional="True" type="text" value="l2"/>
164 <param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="'null'"/> 282 <param label="--p-feat-ext--preprocessor: TEXT [default: 'null']" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
165 <param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="'null'"/> 283 <param label="--p-feat-ext--stop-words: TEXT [default: 'null']" name="pfeatextstopwords" optional="True" type="text" value="null"/>
166 <param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="'null'"/> 284 <param label="--p-feat-ext--strip-accents: TEXT [default: 'null']" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
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'"/> 285 <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"/>
168 <param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="'null'"/> 286 <param label="--p-feat-ext--tokenizer: TEXT [default: 'null']" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
169 </inputs> 287 </inputs>
170 <outputs> 288 <outputs>
171 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/> 289 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
172 </outputs> 290 </outputs>
173 <help><![CDATA[ 291 <help><![CDATA[