comparison qiime2/qiime_diversity_alpha-phylogenetic.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_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic"
3 version="2020.8">
4 <description>Alpha diversity (phylogenetic)</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity alpha-phylogenetic
10
11 --i-table=$itable
12
13 --i-phylogeny=$iphylogeny
14
15 --p-metric=$pmetric
16
17 --o-alpha-diversity=oalphadiversity
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp oalphadiversity.qza $oalphadiversity
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data" />
29 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
30 <param label="--p-metric: " name="pmetric" optional="False" type="select">
31 <option value="faith_pd">faith_pd</option>
32 </param>
33 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
34
35 </inputs>
36
37 <outputs>
38 <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity" />
39
40 </outputs>
41
42 <help><![CDATA[
43 Alpha diversity (phylogenetic)
44 ###############################################################
45
46 Computes a user-specified phylogenetic alpha diversity metric for all
47 samples in a feature table.
48
49 Parameters
50 ----------
51 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
52 The feature table containing the samples for which alpha diversity
53 should be computed.
54 phylogeny : Phylogeny[Rooted]
55 Phylogenetic tree containing tip identifiers that correspond to the
56 feature identifiers in the table. This tree can contain tip ids that
57 are not present in the table, but all feature ids in the table must be
58 present in this tree.
59 metric : Str % Choices('faith_pd')
60 The alpha diversity metric to be computed.
61
62 Returns
63 -------
64 alpha_diversity : SampleData[AlphaDiversity]
65 Vector containing per-sample alpha diversities.
66 ]]></help>
67 <macros>
68 <import>qiime_citation.xml</import>
69 </macros>
70 <expand macro="qiime_citation"/>
71 </tool>