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comparison qiime2/qiime_diversity_beta-phylogenetic.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" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic" version="2019.7"> 2 <tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic"
3 <description> - Beta diversity (phylogenetic)</description> 3 version="2020.8">
4 <requirements> 4 <description>Beta 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 beta-phylogenetic 9 qiime diversity beta-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 #set $pnjobs = '${GALAXY_SLOTS:-4}' 17 #if str($pthreads) != 'None':
15 #if str($pnjobs): 18 --p-threads=$pthreads
16 --p-n-jobs="$pnjobs"
17 #end if 19 #end if
18
19 20
20 #if $pvarianceadjusted: 21 #if $pvarianceadjusted:
21 --p-variance-adjusted 22 --p-variance-adjusted
22 #end if 23 #end if
23 24
24 #if str($palpha): 25 #if str($palpha):
25 --p-alpha="$palpha" 26 --p-alpha=$palpha
26 #end if 27 #end if
27
28 #if $pbypasstips: 28 #if $pbypasstips:
29 --p-bypass-tips 29 --p-bypass-tips
30 #end if 30 #end if
31 31
32 --o-distance-matrix=odistancematrix 32 --o-distance-matrix=odistancematrix
33
34 #if str($examples) != 'None':
35 --examples=$examples
36 #end if
37
33 ; 38 ;
34 cp odistancematrix.qza $odistancematrix 39 cp odistancematrix.qza $odistancematrix
35 ]]></command> 40
36 <inputs> 41 ]]></command>
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"/> 42 <inputs>
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"/> 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" />
39 <param label="--p-metric: " name="pmetric" optional="False" type="select"> 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" />
40 <option value="generalized_unifrac">generalized_unifrac</option> 45 <param label="--p-metric: " name="pmetric" optional="False" type="select">
41 <option value="unweighted_unifrac">unweighted_unifrac</option> 46 <option value="weighted_unifrac">weighted_unifrac</option>
42 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option> 47 <option value="unweighted_unifrac">unweighted_unifrac</option>
43 <option value="weighted_unifrac">weighted_unifrac</option> 48 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
44 </param> 49 <option value="generalized_unifrac">generalized_unifrac</option>
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"/> 50 </param>
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"/> 51 <param label="--p-threads: " name="pthreads" optional="True" type="select">
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"/> 52 <option selected="True" value="None">Selection is Optional</option>
48 </inputs> 53 <option value="Int % Range(1">Int % Range(1</option>
49 <outputs> 54 <option value="None">None</option>
50 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/> 55 </param>
51 </outputs> 56 <param label="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation. [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
52 <help><![CDATA[ 57 <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized. [optional]" name="palpha" optional="False" type="text" />
58 <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]" name="pbypasstips" selected="False" type="boolean" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
65
66 </outputs>
67
68 <help><![CDATA[
53 Beta diversity (phylogenetic) 69 Beta diversity (phylogenetic)
54 ############################# 70 ###############################################################
55 71
56 Computes a user-specified phylogenetic beta diversity metric for all pairs 72 Computes a user-specified phylogenetic beta diversity metric for all pairs
57 of samples in a feature table. 73 of samples in a feature table.
58 74
59 Parameters 75 Parameters
60 ---------- 76 ----------
61 table : FeatureTable[Frequency] 77 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
62 The feature table containing the samples over which beta diversity 78 The feature table containing the samples over which beta diversity
63 should be computed. 79 should be computed.
64 phylogeny : Phylogeny[Rooted] 80 phylogeny : Phylogeny[Rooted]
65 Phylogenetic tree containing tip identifiers that correspond to the 81 Phylogenetic tree containing tip identifiers that correspond to the
66 feature identifiers in the table. This tree can contain tip ids that 82 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 83 are not present in the table, but all feature ids in the table must be
68 present in this tree. 84 present in this tree.
69 metric : Str % Choices('weighted_unifrac', 'generalized_unifrac', 'weighted_normalized_unifrac', 'unweighted_unifrac') 85 metric : Str % Choices('generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'unweighted_unifrac')
70 The beta diversity metric to be computed. 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.
71 variance_adjusted : Bool, optional 91 variance_adjusted : Bool, optional
72 Perform variance adjustment based on Chang et al. BMC Bioinformatics 92 Perform variance adjustment based on Chang et al. BMC Bioinformatics
73 2011. Weights distances based on the proportion of the relative 93 2011. Weights distances based on the proportion of the relative
74 abundance represented between the samples at a given node under 94 abundance represented between the samples at a given node under
75 evaluation. 95 evaluation.
85 time. This has the effect of collapsing the phylogeny, and is analogous 105 time. This has the effect of collapsing the phylogeny, and is analogous
86 (in concept) to moving from 99% to 97% OTUs 106 (in concept) to moving from 99% to 97% OTUs
87 107
88 Returns 108 Returns
89 ------- 109 -------
90 distance_matrix : DistanceMatrix % Properties('phylogenetic') 110 distance_matrix : DistanceMatrix
91 The resulting distance matrix. 111 The resulting distance matrix.
92 ]]></help> 112 ]]></help>
93 <macros> 113 <macros>
94 <import>qiime_citation.xml</import> 114 <import>qiime_citation.xml</import>
95 </macros> 115 </macros>
96 <expand macro="qiime_citation"/> 116 <expand macro="qiime_citation"/>
97 </tool> 117 </tool>