|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_adonis" name="qiime diversity adonis" version="2019.4">
|
|
|
3 <description> - adonis PERMANOVA test for beta group significance</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity adonis
|
|
|
9
|
|
|
10 --i-distance-matrix=$idistancematrix
|
|
|
11
|
|
|
12
|
|
|
13 #def list_dict_to_string(list_dict):
|
|
|
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
15 #for d in list_dict[1:]:
|
|
|
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
|
17 #end for
|
|
|
18 #return $file_list
|
|
|
19 #end def
|
|
|
20
|
|
|
21 --m-metadata-file=$list_dict_to_string("$input_files_mmetadatafile")
|
|
|
22
|
|
|
23
|
|
|
24
|
|
|
25
|
|
|
26 --p-formula="$pformula"
|
|
|
27
|
|
|
28 #if $ppermutations:
|
|
|
29 --p-permutations=$ppermutations
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #set $pnjobs = '${GALAXY_SLOTS:-4}'
|
|
|
33 #if str($pnjobs):
|
|
|
34 --p-n-jobs="$pnjobs"
|
|
|
35 #end if
|
|
|
36
|
|
|
37 --o-visualization=ovisualization
|
|
|
38 ;
|
|
|
39 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
40 && cp -r out/* '$ovisualization.files_path'
|
|
|
41 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
42 ]]></command>
|
|
|
43 <inputs>
|
|
|
44 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
|
|
|
45 <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula 'treatment+block' would test whether the input distance matrix partitions based on 'treatment' and 'block' sample metadata. The formula 'treatment*block' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text"/>
|
|
|
46 <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" min="1" type="integer" value="999"/>
|
|
|
47
|
|
|
48 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
49 <param format="tabular" label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data"/>
|
|
|
50 </repeat>
|
|
|
51 </inputs>
|
|
|
52 <outputs>
|
|
|
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
54 </outputs>
|
|
|
55 <help><![CDATA[
|
|
|
56 adonis PERMANOVA test for beta group significance
|
|
|
57 #################################################
|
|
|
58
|
|
|
59 Determine whether groups of samples are significantly different from one
|
|
|
60 another using the ADONIS permutation-based statistical test in vegan-R. The
|
|
|
61 function partitions sums of squares of a multivariate data set, and is
|
|
|
62 directly analogous to MANOVA (multivariate analysis of variance). This
|
|
|
63 action differs from beta_group_signficance in that it accepts R formulae to
|
|
|
64 perform multi-way ADONIS tests; beta_group_signficance only performs one-
|
|
|
65 way tests. For more details see
|
|
|
66 http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
|
|
|
67
|
|
|
68 Parameters
|
|
|
69 ----------
|
|
|
70 distance_matrix : DistanceMatrix
|
|
|
71 Matrix of distances between pairs of samples.
|
|
|
72 metadata : Metadata
|
|
|
73 Sample metadata containing formula terms.
|
|
|
74 formula : Str
|
|
|
75 Model formula containing only independent terms contained in the sample
|
|
|
76 metadata. These can be continuous variables or factors, and they can
|
|
|
77 have interactions as in a typical R formula. E.g., the formula
|
|
|
78 "treatment+block" would test whether the input distance matrix
|
|
|
79 partitions based on "treatment" and "block" sample metadata. The
|
|
|
80 formula "treatment*block" would test both of those effects as well as
|
|
|
81 their interaction. Enclose formulae in quotes to avoid unpleasant
|
|
|
82 surprises.
|
|
|
83 permutations : Int % Range(1, None), optional
|
|
|
84 The number of permutations to be run when computing p-values.
|
|
|
85
|
|
|
86 Returns
|
|
|
87 -------
|
|
|
88 visualization : Visualization
|
|
|
89 ]]></help>
|
|
|
90 <macros>
|
|
|
91 <import>qiime_citation.xml</import>
|
|
|
92 </macros>
|
|
|
93 <expand macro="qiime_citation"/>
|
|
|
94 </tool>
|
