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comparison qiime2/qiime_diversity-lib_faith-pd.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity-lib_faith-pd" name="qiime diversity-lib faith-pd"
3 version="2020.8">
4 <description>Faith\'s Phylogenetic Diversity</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity-lib faith-pd
10
11 #if $itable:
12 --i-table
13 #end if
14
15 --i-phylogeny=$iphylogeny
16
17 --o-vector=ovector
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp ovector.qza $ovector
25
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which Faith\'s phylogenetic diversity should be computed. Table values will be converted to presence/absence. [required]" name="itable" selected="False" type="boolean" />
29 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
31
32 </inputs>
33
34 <outputs>
35 <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" />
36
37 </outputs>
38
39 <help><![CDATA[
40 Faith\'s Phylogenetic Diversity
41 ###############################################################
42
43 Computes Faith's Phylogenetic Diversity for all samples in a feature table.
44
45 Parameters
46 ----------
47 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
48 The feature table containing the samples for which Faith's phylogenetic
49 diversity should be computed. Table values will be converted to
50 presence/absence.
51 phylogeny : Phylogeny[Rooted]
52 Phylogenetic tree containing tip identifiers that correspond to the
53 feature identifiers in the table. This tree can contain tip ids that
54 are not present in the table, but all feature ids in the table must be
55 present in this tree.
56
57 Returns
58 -------
59 vector : SampleData[AlphaDiversity]
60 Vector containing per-sample values for Faith's Phylogenetic Diversity.
61 ]]></help>
62 <macros>
63 <import>qiime_citation.xml</import>
64 </macros>
65 <expand macro="qiime_citation"/>
66 </tool>