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comparison qiime2-2020.8/qiime_diversity_mantel.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_mantel" name="qiime diversity mantel"
3 version="2020.8">
4 <description>Apply the Mantel test to two distance matrices</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity mantel
10
11 --i-dm1=$idm1
12
13 --i-dm2=$idm2
14
15 #if str($pmethod) != 'None':
16 --p-method=$pmethod
17 #end if
18
19 --p-permutations=$ppermutations
20
21 #if $pintersectids:
22 --p-intersect-ids
23 #end if
24
25 #if str($plabel1):
26 --p-label1=$plabel1
27 #end if
28 #if str($plabel2):
29 --p-label2=$plabel2
30 #end if
31 --o-visualization=ovisualization
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
37 ;
38 cp ofiltereddistancematrix.qza $ofiltereddistancematrix
39
40 ;
41 qiime tools export ovisualization.qzv --output-path out
42 && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
45
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data" />
49 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data" />
50 <param label="--p-method: " name="pmethod" optional="True" type="select">
51 <option selected="True" value="None">Selection is Optional</option>
52 <option value="spearman">spearman</option>
53 <option value="pearson">pearson</option>
54 </param>
55 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" />
56 <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" />
57 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: \'Distance Matrix 1\']" name="plabel1" optional="False" type="text" value="\'Distance Matrix 1\'" />
58 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: \'Distance Matrix 2\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix 2\'" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
62
63 <outputs>
64 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
65
66 </outputs>
67
68 <help><![CDATA[
69 Apply the Mantel test to two distance matrices
70 ###############################################################
71
72 Apply a two-sided Mantel test to identify correlation between two distance
73 matrices. Note: the directionality of the comparison has no bearing on the
74 results. Thus, comparing distance matrix X to distance matrix Y is
75 equivalent to comparing Y to X. Note: the order of samples within the two
76 distance matrices does not need to be the same; the distance matrices will
77 be reordered before applying the Mantel test. See the scikit-bio docs for
78 more details about the Mantel test: http://scikit-
79 bio.org/docs/latest/generated/skbio.stats.distance.mantel
80
81 Parameters
82 ----------
83 dm1 : DistanceMatrix
84 Matrix of distances between pairs of samples.
85 dm2 : DistanceMatrix
86 Matrix of distances between pairs of samples.
87 method : Str % Choices('spearman', 'pearson'), optional
88 The correlation test to be applied in the Mantel test.
89 permutations : Int % Range(0, None), optional
90 The number of permutations to be run when computing p-values. Supplying
91 a value of zero will disable permutation testing and p-values will not
92 be calculated (this results in *much* quicker execution time if
93 p-values are not desired).
94 intersect_ids : Bool, optional
95 If supplied, IDs that are not found in both distance matrices will be
96 discarded before applying the Mantel test. Default behavior is to error
97 on any mismatched IDs.
98 label1 : Str, optional
99 Label for `dm1` in the output visualization.
100 label2 : Str, optional
101 Label for `dm2` in the output visualization.
102
103 Returns
104 -------
105 visualization : Visualization
106 ]]></help>
107 <macros>
108 <import>qiime_citation.xml</import>
109 </macros>
110 <expand macro="qiime_citation"/>
111 </tool>