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comparison qiime_feature-table_core-features.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2018.4">
3 <description> - Identify core features in table</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime feature-table core-features --i-table=$itable
10
11 #if str($cmdconfig) != 'None':
12 --cmd-config=$cmdconfig
13 #end if
14
15 #if $pminfraction:
16 --p-min-fraction=$pminfraction
17 #end if
18
19 #if $pmaxfraction:
20 --p-max-fraction=$pmaxfraction
21 #end if
22 --o-visualization=ovisualization
23 #if $psteps:
24 --p-steps=$psteps
25 #end if
26 ;
27 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
28 && cp -r out/* '$ovisualization.files_path'
29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
30 ]]></command>
31 <inputs>
32 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data"/>
33
34 <param label="--p-min-fraction: 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"/>
35 <param label="--p-max-fraction: 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"/>
36
37 <param label="--p-steps: The number of steps to take between `min_fraction` and `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"/>
38
39 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
40 </inputs>
41 <outputs>
42 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
43 </outputs>
44 <help>
45 <![CDATA[
46 Identify core features in table
47 --------------------------------
48
49 Identify "core" features, which are features observed in a user-defined
50 fraction of the samples. Since the core features are a function of the
51 fraction of samples that the feature must be observed in to be considered
52 core, this is computed over a range of fractions defined by the
53 `min_fraction`, `max_fraction`, and `steps` parameters.
54
55 Parameters
56 ----------
57 table : FeatureTable[Frequency]
58 The feature table to use in core features calculations.
59 min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
60 The minimum fraction of samples that a feature must be observed in for
61 that feature to be considered a core feature.
62 max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
63 The maximum fraction of samples that a feature must be observed in for
64 that feature to be considered a core feature.
65 steps : Int % Range(2, None), optional
66 The number of steps to take between `min_fraction` and `max_fraction`
67 for core features calculations. This parameter has no effect if
68 `min_fraction` and `max_fraction` are the same value.
69
70 Returns
71 -------
72 visualization : Visualization
73 \
74 ]]>
75 </help>
76 </tool>