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comparison qiime2/qiime_gneiss_ilr-hierarchical.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_ilr-hierarchical" name="qiime gneiss ilr-hierarchical"
3 version="2020.8">
4 <description>Isometric Log-ratio Transform applied to a hierarchical clustering</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime gneiss ilr-hierarchical
10
11 --i-table=$itable
12
13 --i-tree=$itree
14
15 --p-pseudocount=$ppseudocount
16
17 --o-balances=obalances
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp obalances.qza $obalances
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | Composition] The feature table containing the samples in which the ilr transform will be performed. [required]" name="itable" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers that defines the Hierarchy partitions of features. Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. This assumes that all of the internal nodes in the tree have labels. [required]" name="itree" optional="False" type="data" />
30 <param label="--p-pseudocount: NUMBER The value to add to zero counts in the feature table. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
32
33 </inputs>
34
35 <outputs>
36 <data format="qza" label="${tool.name} on ${on_string}: balances.qza" name="obalances" />
37
38 </outputs>
39
40 <help><![CDATA[
41 Isometric Log-ratio Transform applied to a hierarchical clustering
42 ###############################################################
43
44 Calculate balances given a hierarchy.
45
46 Parameters
47 ----------
48 table : FeatureTable[Frequency | Composition]
49 The feature table containing the samples in which the ilr transform
50 will be performed.
51 tree : Hierarchy
52 A hierarchy of feature identifiers that defines the partitions of
53 features. Each tip in the hierarchycorresponds to the feature
54 identifiers in the table. This tree can contain tip ids that are not
55 present in the table, but all feature ids in the table must be present
56 in this tree. This assumes that all of the internal nodes in the tree
57 have labels.
58 pseudocount : Float, optional
59 The value to add to zero counts in the feature table.
60
61 Returns
62 -------
63 balances : FeatureTable[Balance]
64 The resulting balances from the ilr transform.
65 ]]></help>
66 <macros>
67 <import>qiime_citation.xml</import>
68 </macros>
69 <expand macro="qiime_citation"/>
70 </tool>