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comparison qiime2/qiime_diversity_mantel.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2018.4">
3 <description> - Apply the Mantel test to two distance matrices</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity mantel --i-dm2=$idm2 --i-dm1=$idm1
9
10 #if $pintersectids:
11 --p-intersect-ids
12 #else
13 --p-no-intersect-ids
14 #end if
15
16 #if str($cmdconfig) != 'None':
17 --cmd-config=$cmdconfig
18 #end if
19
20 #if str($plabel2):
21 --p-label2="$plabel2"
22 #end if
23
24 #if str($plabel1):
25 --p-label1="$plabel1"
26 #end if
27
28 --o-visualization=ovisualization
29
30 #if str($pmethod) != 'None':
31 --p-method=$pmethod
32 #end if
33
34 #if $ppermutations:
35 --p-permutations=$ppermutations
36 #end if
37 ;
38 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
39 && cp -r out/* '$ovisualization.files_path'
40 && mv '$ovisualization.files_path/index.html' '$ovisualization';
41 ]]></command>
42 <inputs>
43 <param format="qza,no_unzip.zip" label="--i-dm1: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idm1" optional="False" type="data"/>
44 <param format="qza,no_unzip.zip" label="--i-dm2: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idm2" optional="False" type="data"/>
45 <param label="--p-method: " name="pmethod" optional="True" type="select">
46 <option selected="True" value="spearman">spearman</option>
47 <option value="pearson">pearson</option>
48 </param>
49 <param label="--p-permutations: 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]" name="ppermutations" optional="True" type="integer" value="999"/>
50 <param label="--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" checked="False" type="boolean"/>
51 <param label="--p-label1: Label for \`dm1\` in the output visualization. [default: Distance Matrix 1]" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
52 <param label="--p-label2: Label for \`dm2\` in the output visualization. [default: Distance Matrix 2]" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
53 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
54 </inputs>
55 <outputs>
56 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
57 </outputs>
58 <help><![CDATA[
59 Apply the Mantel test to two distance matrices
60 ----------------------------------------------
61
62 Apply a two-sided Mantel test to identify correlation between two distance
63 matrices. Note: the directionality of the comparison has no bearing on the
64 results. Thus, comparing distance matrix X to distance matrix Y is
65 equivalent to comparing Y to X. Note: the order of samples within the two
66 distance matrices does not need to be the same; the distance matrices will
67 be reordered before applying the Mantel test. See the scikit-bio docs for
68 more details about the Mantel test: http://scikit-
69 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
70
71 Parameters
72 ----------
73 dm1 : DistanceMatrix
74 Matrix of distances between pairs of samples.
75 dm2 : DistanceMatrix
76 Matrix of distances between pairs of samples.
77 method : Str % Choices({'pearson', 'spearman'}), optional
78 The correlation test to be applied in the Mantel test.
79 permutations : Int % Range(0, None), optional
80 The number of permutations to be run when computing p-values. Supplying
81 a value of zero will disable permutation testing and p-values will not
82 be calculated (this results in *much* quicker execution time if
83 p-values are not desired).
84 intersect_ids : Bool, optional
85 If supplied, IDs that are not found in both distance matrices will be
86 discarded before applying the Mantel test. Default behavior is to error
87 on any mismatched IDs.
88 label1 : Str, optional
89 Label for \`dm1\` in the output visualization.
90 label2 : Str, optional
91 Label for \`dm2\` in the output visualization.
92
93 Returns
94 -------
95 visualization : Visualization
96 \
97 ]]>
98 </help>
99 <macros>
100 <import>qiime_citation.xml</import>
101 </macros>
102 <expand macro="qiime_citation" />
103 </tool>