Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_gneiss_correlation-clustering.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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28:c28331a63dfd | 29:3ba9833030c1 |
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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> |