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comparison qiime2/qiime_diversity_beta-phylogenetic-alt.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-phylogenetic-alt" name="qiime diversity beta-phylogenetic-alt" version="2019.4">
3 <description> - Beta diversity (phylogenetic) - High Performance Computation</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime diversity beta-phylogenetic-alt --i-table=$itable --i-phylogeny=$iphylogeny --p-metric=$pmetric
10
11 #if str($cmdconfig) != 'None':
12 --cmd-config=$cmdconfig
13 #end if
14
15 #if $pbypasstips:
16 --p-bypass-tips
17 #else
18 --p-no-bypass-tips
19 #end if
20
21 #set $pnjobs = '${GALAXY_SLOTS:-4}'
22
23 #if str($pnjobs):
24 --p-n-jobs="$pnjobs"
25 #end if
26
27 --o-distance-matrix=odistancematrix
28
29 #if $pvarianceadjusted:
30 --p-variance-adjusted
31 #else
32 --p-no-variance-adjusted
33 #end if
34
35 #if str($palpha):
36 --p-alpha="$palpha"
37 #end if
38 ;
39 cp odistancematrix.qza $odistancematrix;
40 ]]></command>
41 <inputs>
42 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data"/>
43 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Phylogenetic tree containing tip identifiers that 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"/>
44 <param label="--p-metric: The beta diversity metric to be computed.
45 [required]" name="pmetric" optional="False" type="select">
46 <option selected="True" value="generalized_unifrac">generalized_unifrac</option>
47 <option value="weighted_unifrac">weighted_unifrac</option>
48 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
49 <option value="unweighted_unifrac">unweighted_unifrac</option>
50 </param>
51 <param label="--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" checked="False" type="boolean"/>
52 <param label="--p-alpha: 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="True" type="text"/>
53 <param label="--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" checked="False" type="boolean"/>
54 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
55 </inputs>
56 <outputs>
57 <data format="qza" label="${tool.name} on ${on_string}: distance-matrix.qza" name="odistancematrix"/>
58 </outputs>
59 <help>
60 <![CDATA[
61 Beta diversity (phylogenetic) - High Performance Computation
62 -------------------------------------------------------------
63
64 Computes a user-specified phylogenetic beta diversity metric for all pairs
65 of samples in a feature table. This implementation is recommended for large
66 datasets, otherwise the results are identical to beta_phylogenetic. This
67 method is an implementation of the Strided State UniFrac algorithm.
68 Multiple variants of the UniFrac metric are available, including
69 Generalized UniFrac (Chen et al. 2012), Variance Adjusted UniFrac (Chang et
70 al. 2011), as well as Weighted normalized and unnormalized UniFrac
71 (Lozupone et al. 2007) and unweighted UniFrac (Lozupone et al. 2005)
72
73 Parameters
74 ----------
75 table : FeatureTable[Frequency]
76 The feature table containing the samples over which beta diversity
77 should be computed.
78 phylogeny : Phylogeny[Rooted]
79 Phylogenetic tree containing tip identifiers that correspond to the
80 feature identifiers in the table. This tree can contain tip ids that
81 are not present in the table, but all feature ids in the table must be
82 present in this tree.
83 metric : Str % Choices({'generalized_unifrac', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac'})
84 The beta diversity metric to be computed.
85 variance_adjusted : Bool, optional
86 Perform variance adjustment based on Chang et al. BMC Bioinformatics
87 2011. Weights distances based on the proportion of the relative
88 abundance represented between the samples at a given node under
89 evaluation.
90 alpha : Float % Range(0, 1, inclusive_end=True), optional
91 This parameter is only used when the choice of metric is
92 generalized_unifrac. The value of alpha controls importance of sample
93 proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
94 unweighted UniFrac, but only if the sample proportions are
95 dichotomized.
96 bypass_tips : Bool, optional
97 In a bifurcating tree, the tips make up about 50% of the nodes in a
98 tree. By ignoring them, specificity can be traded for reduced compute
99 time. This has the effect of collapsing the phylogeny, and is analogous
100 (in concept) to moving from 99% to 97% OTUs
101
102 Returns
103 -------
104 distance_matrix : DistanceMatrix % Properties(['phylogenetic'])
105 The resulting distance matrix.
106 ]]>
107 </help>
108 <macros>
109 <import>qiime_citation.xml</import>
110 </macros>
111 <expand macro="qiime_citation" />
112 </tool>