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comparison qiime2-2020.8/qiime_diversity-lib_weighted-unifrac.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity-lib_weighted-unifrac" name="qiime diversity-lib weighted-unifrac"
3 version="2020.8">
4 <description>Weighted Unifrac</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity-lib weighted-unifrac
10
11 --i-table=$itable
12
13 --i-phylogeny=$iphylogeny
14
15 #if str($pthreads) != 'None':
16 --p-threads=$pthreads
17 #end if
18
19 #if $pbypasstips:
20 --p-bypass-tips
21 #end if
22
23 --o-distance-matrix=odistancematrix
24
25 #if str($examples) != 'None':
26 --examples=$examples
27 #end if
28
29 ;
30 cp odistancematrix.qza $odistancematrix
31
32 ]]></command>
33 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table containing the samples for which Weighted Unifrac should be computed. [required]" name="itable" optional="False" type="data" />
35 <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" />
36 <param label="--p-threads: " name="pthreads" optional="True" type="select">
37 <option selected="True" value="None">Selection is Optional</option>
38 <option value="Int % Range(1">Int % Range(1</option>
39 <option value="None">None</option>
40 </param>
41 <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs [default: False]" name="pbypasstips" selected="False" type="boolean" />
42 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
43
44 </inputs>
45
46 <outputs>
47 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
48
49 </outputs>
50
51 <help><![CDATA[
52 Weighted Unifrac
53 ###############################################################
54
55 Compute Weighted Unifrac for each sample in a feature table
56
57 Parameters
58 ----------
59 table : FeatureTable[Frequency | RelativeFrequency]
60 The feature table containing the samples for which Weighted Unifrac
61 should be computed.
62 phylogeny : Phylogeny[Rooted]
63 Phylogenetic tree containing tip identifiers that correspond to the
64 feature identifiers in the table. This tree can contain tip ids that
65 are not present in the table, but all feature ids in the table must be
66 present in this tree.
67 threads : Int % Range(1, None) | Str % Choices('auto'), optional
68 The number of CPU threads to use in performing this calculation. May
69 not exceed the number of available physical cores. If threads = 'auto',
70 one thread will be created for each identified CPU core on the host.
71 bypass_tips : Bool, optional
72 In a bifurcating tree, the tips make up about 50% of the nodes in a
73 tree. By ignoring them, specificity can be traded for reduced compute
74 time. This has the effect of collapsing the phylogeny, and is analogous
75 (in concept) to moving from 99% to 97% OTUs
76
77 Returns
78 -------
79 distance_matrix : DistanceMatrix
80 Distance matrix for Unweighted Unifrac.
81 ]]></help>
82 <macros>
83 <import>qiime_citation.xml</import>
84 </macros>
85 <expand macro="qiime_citation"/>
86 </tool>