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comparison qiime2-2020.8/qiime_sample-classifier_predict-classification.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_predict-classification" name="qiime sample-classifier predict-classification"
3 version="2020.8">
4 <description>Use trained classifier to predict target values for new samples.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime sample-classifier predict-classification
10
11 --i-table=$itable
12
13 --i-sample-estimator=$isampleestimator
14
15 --p-n-jobs=$pnjobs
16
17 --o-predictions=opredictions
18
19 --o-probabilities=oprobabilities
20
21 #if str($examples) != 'None':
22 --examples=$examples
23 #end if
24
25 ;
26 cp oprobabilities.qza $oprobabilities
27
28 ]]></command>
29 <inputs>
30 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data" />
31 <param format="qza,no_unzip.zip" label="--i-sample-estimator: ARTIFACT SampleEstimator[Classifier] Sample classifier trained with fit_classifier. [required]" name="isampleestimator" optional="False" type="data" />
32 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
33
34 </inputs>
35
36 <outputs>
37 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" />
38 <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities" />
39
40 </outputs>
41
42 <help><![CDATA[
43 Use trained classifier to predict target values for new samples.
44 ###############################################################
45
46 Use trained estimator to predict target values for new samples. These will
47 typically be unseen samples, e.g., test data (derived manually or from
48 split_table) or samples with unknown values, but can theoretically be any
49 samples present in a feature table that contain overlapping features with
50 the feature table used to train the estimator.
51
52 Parameters
53 ----------
54 table : FeatureTable[Frequency]
55 Feature table containing all features that should be used for target
56 prediction.
57 sample_estimator : SampleEstimator[Classifier]
58 Sample classifier trained with fit_classifier.
59 n_jobs : Int, optional
60 Number of jobs to run in parallel.
61
62 Returns
63 -------
64 predictions : SampleData[ClassifierPredictions]
65 Predicted target values for each input sample.
66 probabilities : SampleData[Probabilities]
67 Predicted class probabilities for each input sample.
68 ]]></help>
69 <macros>
70 <import>qiime_citation.xml</import>
71 </macros>
72 <expand macro="qiime_citation"/>
73 </tool>