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