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comparison qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children f190567fe3f6
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.4">
3 <description> - Train an almost arbitrary scikit-learn classifier</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime feature-classifier fit-classifier-sklearn
9
10 --i-reference-reads=$ireferencereads
11
12
13 #if str( $id_to_taxonomy_fp.selector ) == 'history'
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp
15 --i-reference-taxonomy '$tax'
16 #else:
17 #set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
18 --i-reference-taxonomy '$tax'
19 #end if
20
21
22 --p-classifier-specification="$pclassifierspecification"
23
24 #if str($iclassweight) != 'None':
25 --i-class-weight=$iclassweight
26 #end if
27
28 --o-classifier=oclassifier
29 ;
30 cp oclassifier.qza $oclassifier
31 ]]></command>
32 <inputs>
33 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/>
34
35 <conditional name="id_to_taxonomy_fp" optional="True">
36 <param name="selector" type="select" label="Reference taxonomy to query">
37 <option value="cached">Public databases</option>
38 <option value="history">Databases from your history</option>
39 </param>
40 <when value="cached">
41 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
42 <options from_data_table="qiime_taxonomy" />
43 </param>
44 </when>
45 <when value="history">
46 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
47 </when>
48 </conditional>
49
50 <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text"/>
51 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
52 </inputs>
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
55 </outputs>
56 <help><![CDATA[
57 rain an almost arbitrary scikit-learn classifier
58 ################################################
59
60 Train a scikit-learn classifier to classify reads.
61
62 Parameters
63 ----------
64 reference_reads : FeatureData[Sequence]
65 \
66
67 reference_taxonomy : FeatureData[Taxonomy]
68 \
69
70 classifier_specification : Str
71 \
72
73 class_weight : FeatureTable[RelativeFrequency], optional
74 \
75
76 Returns
77 -------
78 classifier : TaxonomicClassifier
79 \
80
81 ]]></help>
82 <macros>
83 <import>qiime_citation.xml</import>
84 </macros>
85 <expand macro="qiime_citation"/>
86 </tool>