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comparison qiime2-2020.8/qiime_feature-table_core-features.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-table_core-features" name="qiime feature-table core-features"
3 version="2020.8">
4 <description>Identify core features in table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table core-features
10
11 --i-table=$itable
12
13 --p-min-fraction=$pminfraction
14
15 --p-max-fraction=$pmaxfraction
16
17 --p-steps=$psteps
18
19 --o-visualization=ovisualization
20
21 #if str($examples) != 'None':
22 --examples=$examples
23 #end if
24
25 ;
26 cp oclassifier.qza $oclassifier
27
28 ;
29 qiime tools export ovisualization.qzv --output-path out
30 && mkdir -p '$ovisualization.files_path'
31 && cp -r out/* '$ovisualization.files_path'
32 && mv '$ovisualization.files_path/index.html' '$ovisualization'
33
34 ]]></command>
35 <inputs>
36 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data" />
37 <param exclude_min="True" label="--p-min-fraction: PROPORTION Range(0.0, 1.0, inclusive_start=False) The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" max="1.0" min="0.0" name="pminfraction" optional="True" type="float" value="0.5" />
38 <param exclude_max="False" label="--p-max-fraction: PROPORTION Range(0.0, 1.0, inclusive_end=True) The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" max="1.0" min="0.0" name="pmaxfraction" optional="True" type="float" value="1.0" />
39 <param label="--p-steps: INTEGER The number of steps to take between `min-fraction` and Range(2, None) `max-fraction` for core features calculations. This parameter has no effect if `min-fraction` and `max-fraction` are the same value. [default: 11]" min="2" name="psteps" optional="True" type="integer" value="11" />
40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
41
42 </inputs>
43
44 <outputs>
45 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
46
47 </outputs>
48
49 <help><![CDATA[
50 Identify core features in table
51 ###############################################################
52
53 Identify "core" features, which are features observed in a user-defined
54 fraction of the samples. Since the core features are a function of the
55 fraction of samples that the feature must be observed in to be considered
56 core, this is computed over a range of fractions defined by the
57 `min_fraction`, `max_fraction`, and `steps` parameters.
58
59 Parameters
60 ----------
61 table : FeatureTable[Frequency]
62 The feature table to use in core features calculations.
63 min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
64 The minimum fraction of samples that a feature must be observed in for
65 that feature to be considered a core feature.
66 max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
67 The maximum fraction of samples that a feature must be observed in for
68 that feature to be considered a core feature.
69 steps : Int % Range(2, None), optional
70 The number of steps to take between `min_fraction` and `max_fraction`
71 for core features calculations. This parameter has no effect if
72 `min_fraction` and `max_fraction` are the same value.
73
74 Returns
75 -------
76 visualization : Visualization
77 ]]></help>
78 <macros>
79 <import>qiime_citation.xml</import>
80 </macros>
81 <expand macro="qiime_citation"/>
82 </tool>