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comparison qiime2-2020.8/qiime_feature-classifier_classify-sklearn.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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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> |