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comparison qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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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" version="2018.4">
3 <description>- Train the naive_bayes classifier</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime feature-classifier fit-classifier-naive-bayes
10
11 #if str( $id_to_taxonomy_fp.selector ) == 'history'
12 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
13 --i-reference-taxonomy '$tax'
14 #else:
15 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
16 --i-reference-taxonomy '$tax'
17 #end if
18
19
20 --i-reference-reads=$ireferencereads
21
22 #if $pfeatextnonnegative:
23 --p-feat-ext--non-negative
24 #else
25 --p-no-feat-ext--non-negative
26 #end if
27
28 #if str($pfeatexttokenpattern):
29 #if '__ob__' in str($pfeatexttokenpattern):
30 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('__ob__', '[')
31 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
32 #end if
33 #if 'X' in str($pfeatexttokenpattern):
34 #set $pfeatexttokenpattern_temp = $pfeatexttokenpattern.replace('X', '\\')
35 #set $pfeatexttokenpattern = $pfeatexttokenpattern_temp
36 #end if
37 --p-feat-ext--token-pattern="$pfeatexttokenpattern"
38 #end if
39
40 #if str($pfeatextencoding):
41 --p-feat-ext--encoding="$pfeatextencoding"
42 #end if
43
44 #if $pfeatextnfeatures:
45 --p-feat-ext--n-features=$pfeatextnfeatures
46 #end if
47
48 #if str($pfeatextstopwords):
49 --p-feat-ext--stop-words="$pfeatextstopwords"
50 #end if
51
52 #if str($pfeatextngramrange):
53 #if '__ob__' in str($pfeatextngramrange):
54 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('__ob__', '[')
55 #set $pfeatextngramrange = $pfeatextngramrange_temp
56 #end if
57 #if 'X' in str($pfeatextngramrange):
58 #set $pfeatextngramrange_temp = $pfeatextngramrange.replace('X', '\\')
59 #set $pfeatextngramrange = $pfeatextngramrange_temp
60 #end if
61 --p-feat-ext--ngram-range="$pfeatextngramrange"
62 #end if
63
64 #if str($pfeatextanalyzer):
65 --p-feat-ext--analyzer="$pfeatextanalyzer"
66 #end if
67
68 #if $pclassifyalpha:
69 --p-classify--alpha=$pclassifyalpha
70 #end if
71
72 #if str($cmdconfig) != 'None':
73 --cmd-config=$cmdconfig
74 #end if
75
76 #if $pclassifyfitprior:
77 --p-classify--fit-prior
78 #else
79 --p-no-classify--fit-prior
80 #end if
81
82 #if $pfeatextbinary:
83 --p-feat-ext--binary
84 #else
85 --p-no-feat-ext--binary
86 #end if
87
88 #if str($iclassweight) != 'None':
89 --i-class-weight=$iclassweight
90 #end if
91
92 #if str($pfeatextpreprocessor):
93 --p-feat-ext--preprocessor="$pfeatextpreprocessor"
94 #end if
95
96 #if $pfeatextalternatesign:
97 --p-feat-ext--alternate-sign
98 #else
99 --p-no-feat-ext--alternate-sign
100 #end if
101
102 #if $pclassifychunksize:
103 --p-classify--chunk-size=$pclassifychunksize
104 #end if
105
106 #if str($pclassifyclassprior):
107 --p-classify--class-prior="$pclassifyclassprior"
108 #end if
109
110 #if str($pmemory):
111 --p-memory="$pmemory"
112 #end if
113
114 #if $pfeatextlowercase:
115 --p-feat-ext--lowercase
116 #else
117 --p-no-feat-ext--lowercase
118 #end if
119
120 #if str($pfeatextinput):
121 --p-feat-ext--input="$pfeatextinput"
122 #end if
123
124 #if str($pfeatexttokenizer):
125 --p-feat-ext--tokenizer="$pfeatexttokenizer"
126 #end if
127 --o-classifier=oclassifier
128 #if str($pfeatextnorm):
129 --p-feat-ext--norm="$pfeatextnorm"
130 #end if
131
132 #if str($pfeatextdecodeerror):
133 --p-feat-ext--decode-error="$pfeatextdecodeerror"
134 #end if
135
136 #if str($pfeatextstripaccents):
137 --p-feat-ext--strip-accents="$pfeatextstripaccents"
138 #end if
139 ;
140 cp oclassifier.qza $oclassifier;
141 ]]>
142 </command>
143 <inputs>
144 <param format="qza,no_unzip.zip" label="--i-reference-reads: FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
145
146 <conditional name="id_to_taxonomy_fp" optional="True">
147 <param name="selector" type="select" label="Reference taxonomy to query">
148 <option value="cached">Public databases</option>
149 <option value="history">Databases from your history</option>
150 </param>
151 <when value="cached">
152 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
153 <options from_data_table="qiime_taxonomy" />
154 </param>
155 </when>
156 <when value="history">
157 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
158 </when>
159 </conditional>
160
161 <param format="qza,no_unzip.zip" label="--i-class-weight: FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
162
163 <param label="--p-classify--alpha: [default: 0.01]" name="pclassifyalpha" optional="True" type="float" value="0.01"/>
164 <param label="--p-classify--chunk-size: [default: 20000]" name="pclassifychunksize" optional="True" type="integer" value="20000"/>
165
166 <param label="--p-classify--class-prior: [default: null]" name="pclassifyclassprior" optional="True" type="text" value="null"/>
167 <param label="--p-classify--fit-prior: --p-no-classify--fit-prior [default: False]" name="pclassifyfitprior" checked="False" type="boolean"/>
168
169 <param label="--p-feat-ext--alternate-sign: --p-no-feat-ext--alternate-sign [default: False]" name="pfeatextalternatesign" checked="False" type="boolean"/>
170
171 <param label="--p-feat-ext--analyzer: [default: char_wb]" name="pfeatextanalyzer" optional="True" type="text" value="char_wb"/>
172 <param label="--p-feat-ext--binary: --p-no-feat-ext--binary [default: False]" name="pfeatextbinary" checked="False" type="boolean"/>
173
174 <param label="--p-feat-ext--decode-error: [default: strict]" name="pfeatextdecodeerror" optional="True" type="text" value="strict"/>
175
176 <param label="--p-feat-ext--encoding: [default: utf-8]" name="pfeatextencoding" optional="True" type="text" value="utf-8"/>
177 <param label="--p-feat-ext--input: [default: content]" name="pfeatextinput" optional="True" type="text" value="content"/>
178 <param label="--p-feat-ext--lowercase: --p-no-feat-ext--lowercase [default: True]" name="pfeatextlowercase" checked="True" type="boolean"/>
179
180 <param label="--p-feat-ext--n-features: [default: 8192]" name="pfeatextnfeatures" optional="True" type="integer" value="8192"/>
181
182 <param label="--p-feat-ext--ngram-range: [default: [8, 8]]" name="pfeatextngramrange" optional="True" type="text" value="[8, 8]"/>
183 <param label="--p-feat-ext--non-negative: --p-no-feat-ext--non-negative [default: False]" name="pfeatextnonnegative" checked="False" type="boolean"/>
184
185 <param label="--p-feat-ext--norm: [default: l2]" name="pfeatextnorm" optional="True" type="text" value="l2"/>
186 <param label="--p-feat-ext--preprocessor: [default: null]" name="pfeatextpreprocessor" optional="True" type="text" value="null"/>
187
188 <param label="--p-feat-ext--stop-words: [default: null]" name="pfeatextstopwords" optional="True" type="text" value="null"/>
189 <param label="--p-feat-ext--strip-accents: [default: null]" name="pfeatextstripaccents" optional="True" type="text" value="null"/>
190
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"/>
192
193 <param label="--p-feat-ext--tokenizer: [default: null]" name="pfeatexttokenizer" optional="True" type="text" value="null"/>
194
195 <param label="--p-memory: [default: null]" name="pmemory" optional="True" type="text" value="null"/>
196
197 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
198 </inputs>
199 <outputs>
200 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
201 </outputs>
202 <help>
203 <![CDATA[
204 Train the naive_bayes classifier
205 --------------------------------
206
207 Create a scikit-learn naive_bayes classifier for reads
208
209 Parameters
210 ----------
211 reference_reads : FeatureData[Sequence]
212 \
213 reference_taxonomy : FeatureData[Taxonomy]
214 \
215 class_weight : FeatureTable[RelativeFrequency], optional
216 \
217 classify__alpha : Float, optional
218 \
219 classify__chunk_size : Int, optional
220 \
221 classify__class_prior : Str, optional
222 \
223 classify__fit_prior : Bool, optional
224 \
225 feat_ext__alternate_sign : Bool, optional
226 \
227 feat_ext__analyzer : Str, optional
228 \
229 feat_ext__binary : Bool, optional
230 \
231 feat_ext__decode_error : Str, optional
232 \
233 feat_ext__encoding : Str, optional
234 \
235 feat_ext__input : Str, optional
236 \
237 feat_ext__lowercase : Bool, optional
238 \
239 feat_ext__n_features : Int, optional
240 \
241 feat_ext__ngram_range : Str, optional
242 \
243 feat_ext__non_negative : Bool, optional
244 \
245 feat_ext__norm : Str, optional
246 \
247 feat_ext__preprocessor : Str, optional
248 \
249 feat_ext__stop_words : Str, optional
250 \
251 feat_ext__strip_accents : Str, optional
252 \
253 feat_ext__token_pattern : Str, optional
254 \
255 feat_ext__tokenizer : Str, optional
256 \
257 memory : Str, optional
258 \
259
260 Returns
261 -------
262 classifier : TaxonomicClassifier
263 \
264 ]]>
265 </help>
266 <macros>
267 <import>qiime_citation.xml</import>
268 </macros>
269 <expand macro="qiime_citation" />
270 </tool>