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comparison qiime2-2020.8/qiime_diversity_beta-phylogenetic.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic"
3 version="2020.8">
4 <description>Beta diversity (phylogenetic)</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity beta-phylogenetic
10
11 --i-table=$itable
12
13 --i-phylogeny=$iphylogeny
14
15 --p-metric=$pmetric
16
17 #if str($pthreads) != 'None':
18 --p-threads=$pthreads
19 #end if
20
21 #if $pvarianceadjusted:
22 --p-variance-adjusted
23 #end if
24
25 #if str($palpha):
26 --p-alpha=$palpha
27 #end if
28 #if $pbypasstips:
29 --p-bypass-tips
30 #end if
31
32 --o-distance-matrix=odistancematrix
33
34 #if str($examples) != 'None':
35 --examples=$examples
36 #end if
37
38 ;
39 cp odistancematrix.qza $odistancematrix
40
41 ]]></command>
42 <inputs>
43 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data" />
44 <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" />
45 <param label="--p-metric: " name="pmetric" optional="False" type="select">
46 <option value="weighted_unifrac">weighted_unifrac</option>
47 <option value="unweighted_unifrac">unweighted_unifrac</option>
48 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
49 <option value="generalized_unifrac">generalized_unifrac</option>
50 </param>
51 <param label="--p-threads: " name="pthreads" optional="True" type="select">
52 <option selected="True" value="None">Selection is Optional</option>
53 <option value="Int % Range(1">Int % Range(1</option>
54 <option value="None">None</option>
55 </param>
56 <param label="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
57 <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]" name="palpha" optional="False" type="text" />
58 <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]" name="pbypasstips" selected="False" type="boolean" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
65
66 </outputs>
67
68 <help><![CDATA[
69 Beta diversity (phylogenetic)
70 ###############################################################
71
72 Computes a user-specified phylogenetic beta diversity metric for all pairs
73 of samples in a feature table.
74
75 Parameters
76 ----------
77 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
78 The feature table containing the samples over which beta diversity
79 should be computed.
80 phylogeny : Phylogeny[Rooted]
81 Phylogenetic tree containing tip identifiers that correspond to the
82 feature identifiers in the table. This tree can contain tip ids that
83 are not present in the table, but all feature ids in the table must be
84 present in this tree.
85 metric : Str % Choices('generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'unweighted_unifrac')
86 The beta diversity metric to be computed.
87 threads : Int % Range(1, None) | Str % Choices('auto'), optional
88 The number of CPU threads to use in performing this calculation. May
89 not exceed the number of available physical cores. If threads = 'auto',
90 one thread will be created for each identified CPU core on the host.
91 variance_adjusted : Bool, optional
92 Perform variance adjustment based on Chang et al. BMC Bioinformatics
93 2011. Weights distances based on the proportion of the relative
94 abundance represented between the samples at a given node under
95 evaluation.
96 alpha : Float % Range(0, 1, inclusive_end=True), optional
97 This parameter is only used when the choice of metric is
98 generalized_unifrac. The value of alpha controls importance of sample
99 proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
100 unweighted UniFrac, but only if the sample proportions are
101 dichotomized.
102 bypass_tips : Bool, optional
103 In a bifurcating tree, the tips make up about 50% of the nodes in a
104 tree. By ignoring them, specificity can be traded for reduced compute
105 time. This has the effect of collapsing the phylogeny, and is analogous
106 (in concept) to moving from 99% to 97% OTUs
107
108 Returns
109 -------
110 distance_matrix : DistanceMatrix
111 The resulting distance matrix.
112 ]]></help>
113 <macros>
114 <import>qiime_citation.xml</import>
115 </macros>
116 <expand macro="qiime_citation"/>
117 </tool>