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comparison qiime2/qiime_feature-classifier_fit-classifier-naive-bayes.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
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
32 #end if 37 #end if
33 38
34 39
35 40
117 122
118 #if $pnofeatextlowercase: 123 #if $pnofeatextlowercase:
119 --p-no-feat-ext--lowercase 124 --p-no-feat-ext--lowercase
120 #end if 125 #end if
121 126
122 #if $pfeatextnfeatures: 127 #if str($pfeatextnfeatures):
123 --p-feat-ext--n-features=$pfeatextnfeatures 128 --p-feat-ext--n-features=$pfeatextnfeatures
124 #end if 129 #end if
125 130
126 131
127 132