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comparison qiime2/qiime_diversity_adonis.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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>