|
2
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.4">
|
|
|
3 <description> - Identify core features in table</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime feature-table core-features
|
|
|
9
|
|
|
10 --i-table=$itable
|
|
|
11
|
|
4
|
12 #if str($pminfraction):
|
|
2
|
13 --p-min-fraction=$pminfraction
|
|
|
14 #end if
|
|
|
15
|
|
4
|
16 #if str($pmaxfraction):
|
|
2
|
17 --p-max-fraction=$pmaxfraction
|
|
|
18 #end if
|
|
|
19
|
|
4
|
20 #if str($psteps):
|
|
2
|
21 --p-steps=$psteps
|
|
|
22 #end if
|
|
|
23
|
|
|
24 --o-visualization=ovisualization
|
|
|
25 ;
|
|
|
26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
27 && cp -r out/* '$ovisualization.files_path'
|
|
|
28 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
29 ]]></command>
|
|
|
30 <inputs>
|
|
|
31 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data"/>
|
|
|
32 <param label="--p-min-fraction: PROPORTION Range(0.0, 1.0, inclusive_start=False) The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" name="pminfraction" optional="True" type="float" value="0.5"/>
|
|
|
33 <param label="--p-max-fraction: PROPORTION Range(0.0, 1.0, inclusive_end=True) The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" name="pmaxfraction" optional="True" type="float" value="1.0"/>
|
|
|
34 <param label="--p-steps: INTEGER The number of steps to take between `min-fraction` and Range(2, None) `max-fraction` for core features calculations. This parameter has no effect if `min-fraction` and `max-fraction` are the same value. [default: 11]" name="psteps" optional="True" type="integer" value="11"/>
|
|
|
35 </inputs>
|
|
|
36 <outputs>
|
|
|
37 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
38 </outputs>
|
|
|
39 <help><![CDATA[
|
|
|
40 Train an almost arbitrary scikit-learn classifier
|
|
|
41 #################################################
|
|
|
42
|
|
|
43 Train a scikit-learn classifier to classify reads.
|
|
|
44
|
|
|
45 Parameters
|
|
|
46 ----------
|
|
|
47 reference_reads : FeatureData[Sequence]
|
|
|
48 \
|
|
|
49
|
|
|
50 reference_taxonomy : FeatureData[Taxonomy]
|
|
|
51 \
|
|
|
52
|
|
|
53 classifier_specification : Str
|
|
|
54 \
|
|
|
55
|
|
|
56 class_weight : FeatureTable[RelativeFrequency], optional
|
|
|
57 \
|
|
|
58
|
|
|
59 Returns
|
|
|
60 -------
|
|
|
61 classifier : TaxonomicClassifier
|
|
|
62 \
|
|
|
63
|
|
|
64 ]]></help>
|
|
|
65 <macros>
|
|
|
66 <import>qiime_citation.xml</import>
|
|
|
67 </macros>
|
|
|
68 <expand macro="qiime_citation"/>
|
|
|
69 </tool>
|
