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comparison qiime2/qiime_diversity_alpha-phylogenetic.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic" version="2019.7"> 2 <tool id="qiime_diversity_alpha-phylogenetic" name="qiime diversity alpha-phylogenetic"
3 <description> - Alpha diversity (phylogenetic)</description> 3 version="2020.8">
4 <requirements> 4 <description>Alpha diversity (phylogenetic)</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime diversity alpha-phylogenetic 9 qiime diversity alpha-phylogenetic
9 10
10 --i-table=$itable 11 --i-table=$itable
12
11 --i-phylogeny=$iphylogeny 13 --i-phylogeny=$iphylogeny
14
12 --p-metric=$pmetric 15 --p-metric=$pmetric
13 16
14 --o-alpha-diversity=oalphadiversity 17 --o-alpha-diversity=oalphadiversity
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
15 ; 23 ;
16 cp oalphadiversity.qza $oalphadiversity 24 cp oalphadiversity.qza $oalphadiversity
17 ]]></command> 25
18 <inputs> 26 ]]></command>
19 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data"/> 27 <inputs>
20 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data"/> 28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data" />
21 <param label="--p-metric: " name="pmetric" optional="False" type="select"> 29 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
22 <option value="faith_pd">faith_pd</option> 30 <param label="--p-metric: " name="pmetric" optional="False" type="select">
23 </param> 31 <option value="faith_pd">faith_pd</option>
24 </inputs> 32 </param>
25 <outputs> 33 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
26 <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/> 34
27 </outputs> 35 </inputs>
28 <help><![CDATA[ 36
37 <outputs>
38 <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity" />
39
40 </outputs>
41
42 <help><![CDATA[
29 Alpha diversity (phylogenetic) 43 Alpha diversity (phylogenetic)
30 ############################## 44 ###############################################################
31 45
32 Computes a user-specified phylogenetic alpha diversity metric for all 46 Computes a user-specified phylogenetic alpha diversity metric for all
33 samples in a feature table. 47 samples in a feature table.
34 48
35 Parameters 49 Parameters
36 ---------- 50 ----------
37 table : FeatureTable[Frequency] 51 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
38 The feature table containing the samples for which alpha diversity 52 The feature table containing the samples for which alpha diversity
39 should be computed. 53 should be computed.
40 phylogeny : Phylogeny[Rooted] 54 phylogeny : Phylogeny[Rooted]
41 Phylogenetic tree containing tip identifiers that correspond to the 55 Phylogenetic tree containing tip identifiers that correspond to the
42 feature identifiers in the table. This tree can contain tip ids that 56 feature identifiers in the table. This tree can contain tip ids that
45 metric : Str % Choices('faith_pd') 59 metric : Str % Choices('faith_pd')
46 The alpha diversity metric to be computed. 60 The alpha diversity metric to be computed.
47 61
48 Returns 62 Returns
49 ------- 63 -------
50 alpha_diversity : SampleData[AlphaDiversity] % Properties('phylogenetic') 64 alpha_diversity : SampleData[AlphaDiversity]
51 Vector containing per-sample alpha diversities. 65 Vector containing per-sample alpha diversities.
52 ]]></help> 66 ]]></help>
53 <macros> 67 <macros>
54 <import>qiime_citation.xml</import> 68 <import>qiime_citation.xml</import>
55 </macros> 69 </macros>
56 <expand macro="qiime_citation"/> 70 <expand macro="qiime_citation"/>
57 </tool> 71 </tool>