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comparison qiime2/qiime_feature-classifier_fit-classifier-sklearn.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn" version="2019.7"> 2 <tool id="qiime_feature-classifier_fit-classifier-sklearn" name="qiime feature-classifier fit-classifier-sklearn"
3 <description> - Train an almost arbitrary scikit-learn classifier</description> 3 version="2020.8">
4 <requirements> 4 <description>Train an almost arbitrary scikit-learn classifier</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime feature-classifier fit-classifier-sklearn 9 qiime feature-classifier fit-classifier-sklearn
9 10
10 --i-reference-reads=$ireferencereads 11 --i-reference-reads=$ireferencereads
11 12
13 --i-reference-taxonomy=$ireferencetaxonomy
12 14
13 #if str( $id_to_taxonomy_fp.selector ) == 'history' 15 #if str($iclassweight) != 'None':
14 #set $tax = $id_to_taxonomy_fp.taxonomy_fp 16 --i-class-weight=$iclassweight
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 17 #end if
20 18
19 --p-classifier-specification=$pclassifierspecification
21 20
22 --p-classifier-specification="$pclassifierspecification" 21 --o-classifier=oclassifier
23 22
24 #if str($iclassweight) != 'None': 23 #if str($examples) != 'None':
25 --i-class-weight=$iclassweight 24 --examples=$examples
26 #end if 25 #end if
27 26
28 --o-classifier=oclassifier
29 ; 27 ;
30 cp oclassifier.qza $oclassifier 28 cp oclassifier.qza $oclassifier
31 ]]></command> 29
32 <inputs> 30 ]]></command>
33 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data"/> 31 <inputs>
34 32 <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] [required]" name="ireferencereads" optional="False" type="data" />
35 <conditional name="id_to_taxonomy_fp" optional="True"> 33 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] [required]" name="ireferencetaxonomy" optional="False" type="data" />
36 <param name="selector" type="select" label="Reference taxonomy to query"> 34 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="False" type="data" />
37 <option value="cached">Public databases</option> 35 <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text" />
38 <option value="history">Databases from your history</option> 36 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
39 </param> 37
40 <when value="cached"> 38 </inputs>
41 <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True"> 39
42 <options from_data_table="qiime_taxonomy" /> 40 <outputs>
43 </param> 41 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier" />
44 </when> 42
45 <when value="history"> 43 </outputs>
46 <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" /> 44
47 </when> 45 <help><![CDATA[
48 </conditional> 46 Train an almost arbitrary scikit-learn classifier
49 47 ###############################################################
50 <param label="--p-classifier-specification: TEXT [required]" name="pclassifierspecification" optional="False" type="text"/>
51 <param format="qza,no_unzip.zip" label="--i-class-weight: ARTIFACT FeatureTable[RelativeFrequency] [optional]" name="iclassweight" optional="True" type="data"/>
52 </inputs>
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: classifier.qza" name="oclassifier"/>
55 </outputs>
56 <help><![CDATA[
57 rain an almost arbitrary scikit-learn classifier
58 ################################################
59 48
60 Train a scikit-learn classifier to classify reads. 49 Train a scikit-learn classifier to classify reads.
61 50
62 Parameters 51 Parameters
63 ---------- 52 ----------
64 reference_reads : FeatureData[Sequence] 53 reference_reads : FeatureData[Sequence]
65 \
66
67 reference_taxonomy : FeatureData[Taxonomy] 54 reference_taxonomy : FeatureData[Taxonomy]
68 \
69
70 classifier_specification : Str 55 classifier_specification : Str
71 \
72
73 class_weight : FeatureTable[RelativeFrequency], optional 56 class_weight : FeatureTable[RelativeFrequency], optional
74 \
75 57
76 Returns 58 Returns
77 ------- 59 -------
78 classifier : TaxonomicClassifier 60 classifier : TaxonomicClassifier
79 \ 61 ]]></help>
80 62 <macros>
81 ]]></help>
82 <macros>
83 <import>qiime_citation.xml</import> 63 <import>qiime_citation.xml</import>
84 </macros> 64 </macros>
85 <expand macro="qiime_citation"/> 65 <expand macro="qiime_citation"/>
86 </tool> 66 </tool>