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comparison qiime2-2020.8/qiime_feature-classifier_classify-sklearn.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-classifier_classify-sklearn" name="qiime feature-classifier classify-sklearn"
3 version="2020.8">
4 <description>Pre-fitted sklearn-based taxonomy classifier</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-classifier classify-sklearn
10
11 --i-reads=$ireads
12
13 --i-classifier=$iclassifier
14
15 --p-n-jobs=$pnjobs
16
17 #if str($pconfidence) != 'None':
18 --p-confidence=$pconfidence
19 #end if
20
21 #if str($preadorientation) != 'None':
22 --p-read-orientation=$preadorientation
23 #end if
24
25 --o-classification=oclassification
26
27 #if str($examples) != 'None':
28 --examples=$examples
29 #end if
30
31 ;
32 cp oclassification.qza $oclassification
33
34 ]]></command>
35 <inputs>
36 <param format="qza,no_unzip.zip" label="--i-reads: ARTIFACT FeatureData[Sequence] The feature data to be classified. [required]" name="ireads" optional="False" type="data" />
37 <param format="qza,no_unzip.zip" label="--i-classifier: ARTIFACT TaxonomicClassifier The taxonomic classifier for classifying the reads. [required]" name="iclassifier" optional="False" type="data" />
38 <param label="--p-confidence: " name="pconfidence" optional="True" type="select">
39 <option selected="True" value="None">Selection is Optional</option>
40 <option value="Float % Range(0">Float % Range(0</option>
41 <option value="1">1</option>
42 <option value="inclusive_end=True">inclusive_end=True</option>
43 </param>
44 <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
45 <option selected="True" value="None">Selection is Optional</option>
46 <option value="same">same</option>
47 <option value="reverse-complement">reverse-complement</option>
48 <option value="auto">auto</option>
49 </param>
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
51
52 </inputs>
53
54 <outputs>
55 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
56
57 </outputs>
58
59 <help><![CDATA[
60 Pre-fitted sklearn-based taxonomy classifier
61 ###############################################################
62
63 Classify reads by taxon using a fitted classifier.
64
65 Parameters
66 ----------
67 reads : FeatureData[Sequence]
68 The feature data to be classified.
69 classifier : TaxonomicClassifier
70 The taxonomic classifier for classifying the reads.
71 reads_per_batch : Int % Range(0, None), optional
72 Number of reads to process in each batch. If "auto", this parameter is
73 autoscaled to min( number of query sequences / n_jobs, 20000).
74 n_jobs : Int, optional
75 The maximum number of concurrently worker processes. If -1 all CPUs are
76 used. If 1 is given, no parallel computing code is used at all, which
77 is useful for debugging. For n_jobs below -1, (n_cpus + 1 + n_jobs) are
78 used. Thus for n_jobs = -2, all CPUs but one are used.
79 pre_dispatch : Str, optional
80 "all" or expression, as in "3*n_jobs". The number of batches (of tasks)
81 to be pre-dispatched.
82 confidence : Float % Range(0, 1, inclusive_end=True) | Str % Choices('disable'), optional
83 Confidence threshold for limiting taxonomic depth. Set to "disable" to
84 disable confidence calculation, or 0 to calculate confidence but not
85 apply it to limit the taxonomic depth of the assignments.
86 read_orientation : Str % Choices('same', 'reverse-complement', 'auto'), optional
87 Direction of reads with respect to reference sequences. same will cause
88 reads to be classified unchanged; reverse-complement will cause reads
89 to be reversed and complemented prior to classification. "auto" will
90 autodetect orientation based on the confidence estimates for the first
91 100 reads.
92
93 Returns
94 -------
95 classification : FeatureData[Taxonomy]
96 ]]></help>
97 <macros>
98 <import>qiime_citation.xml</import>
99 </macros>
100 <expand macro="qiime_citation"/>
101 </tool>