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comparison qiime2/qiime_diversity_beta-phylogenetic.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" name="qiime diversity beta-phylogenetic" version="2019.4">
3 <description> - Beta diversity (phylogenetic)</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-phylogenetic
9
10 --i-table=$itable
11 --i-phylogeny=$iphylogeny
12 --p-metric=$pmetric
13
14 #set $pnjobs = '${GALAXY_SLOTS:-4}'
15 #if str($pnjobs):
16 --p-n-jobs="$pnjobs"
17 #end if
18
19
20 #if $pvarianceadjusted:
21 --p-variance-adjusted
22 #end if
23
24 #if str($palpha):
25 --p-alpha="$palpha"
26 #end if
27
28 #if $pbypasstips:
29 --p-bypass-tips
30 #end if
31
32 --o-distance-matrix=odistancematrix
33 ;
34 cp odistancematrix.qza $odistancematrix
35 ]]></command>
36 <inputs>
37 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed. [required]" name="itable" optional="False" type="data"/>
38 <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"/>
39 <param label="--p-metric: " name="pmetric" optional="False" type="select">
40 <option value="generalized_unifrac">generalized_unifrac</option>
41 <option value="unweighted_unifrac">unweighted_unifrac</option>
42 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
43 <option value="weighted_unifrac">weighted_unifrac</option>
44 </param>
45 <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" selected="False" type="boolean"/>
46 <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="True" min="0" max="1" exclude_max="False" type="float"/>
47 <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" selected="False" type="boolean"/>
48 </inputs>
49 <outputs>
50 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
51 </outputs>
52 <help><![CDATA[
53 Beta diversity (phylogenetic)
54 #############################
55
56 Computes a user-specified phylogenetic beta diversity metric for all pairs
57 of samples in a feature table.
58
59 Parameters
60 ----------
61 table : FeatureTable[Frequency]
62 The feature table containing the samples over which beta diversity
63 should be computed.
64 phylogeny : Phylogeny[Rooted]
65 Phylogenetic tree containing tip identifiers that correspond to the
66 feature identifiers in the table. This tree can contain tip ids that
67 are not present in the table, but all feature ids in the table must be
68 present in this tree.
69 metric : Str % Choices('weighted_unifrac', 'generalized_unifrac', 'weighted_normalized_unifrac', 'unweighted_unifrac')
70 The beta diversity metric to be computed.
71 variance_adjusted : Bool, optional
72 Perform variance adjustment based on Chang et al. BMC Bioinformatics
73 2011. Weights distances based on the proportion of the relative
74 abundance represented between the samples at a given node under
75 evaluation.
76 alpha : Float % Range(0, 1, inclusive_end=True), optional
77 This parameter is only used when the choice of metric is
78 generalized_unifrac. The value of alpha controls importance of sample
79 proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to
80 unweighted UniFrac, but only if the sample proportions are
81 dichotomized.
82 bypass_tips : Bool, optional
83 In a bifurcating tree, the tips make up about 50% of the nodes in a
84 tree. By ignoring them, specificity can be traded for reduced compute
85 time. This has the effect of collapsing the phylogeny, and is analogous
86 (in concept) to moving from 99% to 97% OTUs
87
88 Returns
89 -------
90 distance_matrix : DistanceMatrix % Properties('phylogenetic')
91 The resulting distance matrix.
92 ]]></help>
93 <macros>
94 <import>qiime_citation.xml</import>
95 </macros>
96 <expand macro="qiime_citation"/>
97 </tool>