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comparison qiime2-2020.8/qiime_gneiss_correlation-clustering.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_correlation-clustering" name="qiime gneiss correlation-clustering"
3 version="2020.8">
4 <description>Hierarchical clustering using feature correlation.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime gneiss correlation-clustering
10
11 --i-table=$itable
12
13 --p-pseudocount=$ppseudocount
14
15 --o-clustering=oclustering
16
17 #if str($examples) != 'None':
18 --examples=$examples
19 #end if
20
21 ;
22 cp oclustering.qza $oclustering
23
24 ]]></command>
25 <inputs>
26 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples in which the columns will be clustered. [required]" name="itable" optional="False" type="data" />
27 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
28 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
29
30 </inputs>
31
32 <outputs>
33 <data format="qza" label="${tool.name} on ${on_string}: clustering.qza" name="oclustering" />
34
35 </outputs>
36
37 <help><![CDATA[
38 Hierarchical clustering using feature correlation.
39 ###############################################################
40
41 Build a bifurcating tree that represents a hierarchical clustering of
42 features. The hiearchical clustering uses Ward hierarchical clustering
43 based on the degree of proportionality between features.
44
45 Parameters
46 ----------
47 table : FeatureTable[Frequency]
48 The feature table containing the samples in which the columns will be
49 clustered.
50 pseudocount : Float, optional
51 The value to add to zero counts in the feature table.
52
53 Returns
54 -------
55 clustering : Hierarchy
56 A hierarchy of feature identifiers where each tip corresponds to the
57 feature identifiers in the table. This tree can contain tip ids that
58 are not present in the table, but all feature ids in the table must be
59 present in this tree.
60 ]]></help>
61 <macros>
62 <import>qiime_citation.xml</import>
63 </macros>
64 <expand macro="qiime_citation"/>
65 </tool>