Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_diversity_adonis.xml @ 20:d93d8888f0b0 draft
Uploaded
author | florianbegusch |
---|---|
date | Fri, 04 Sep 2020 12:44:24 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
19:6c48f8d82424 | 20:d93d8888f0b0 |
---|---|
1 <?xml version="1.0" ?> | |
2 <tool id="qiime_diversity_adonis" name="qiime diversity adonis" | |
3 version="2020.8"> | |
4 <description>adonis PERMANOVA test for beta group significance</description> | |
5 <requirements> | |
6 <requirement type="package" version="2020.8">qiime2</requirement> | |
7 </requirements> | |
8 <command><![CDATA[ | |
9 qiime diversity adonis | |
10 | |
11 --i-distance-matrix=$idistancematrix | |
12 # if $input_files_mmetadatafile: | |
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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
17 # end for | |
18 # return $file_list | |
19 # end def | |
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
21 # end if | |
22 | |
23 --p-formula=$pformula | |
24 | |
25 --p-permutations=$ppermutations | |
26 | |
27 --p-n-jobs=$pnjobs | |
28 | |
29 --o-visualization=ovisualization | |
30 | |
31 #if str($examples) != 'None': | |
32 --examples=$examples | |
33 #end if | |
34 | |
35 ; | |
36 cp osubsampledsequences.qza $osubsampledsequences | |
37 | |
38 ; | |
39 qiime tools export ovisualization.qzv --output-path out | |
40 && mkdir -p '$ovisualization.files_path' | |
41 && cp -r out/* '$ovisualization.files_path' | |
42 && mv '$ovisualization.files_path/index.html' '$ovisualization' | |
43 | |
44 ; | |
45 qiime tools export ovisualization.qzv --output-path out | |
46 && mkdir -p '$ovisualization.files_path' | |
47 && cp -r out/* '$ovisualization.files_path' | |
48 && mv '$ovisualization.files_path/index.html' '$ovisualization' | |
49 | |
50 ]]></command> | |
51 <inputs> | |
52 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" /> | |
53 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> | |
54 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple Sample metadata containing formula terms. arguments will be merged) [required]" name="additional_input" optional="False" type="data" /> | |
55 </repeat> | |
56 <param label="--p-formula: TEXT Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises. [required]" name="pformula" optional="False" type="text" /> | |
57 <param label="--p-permutations: INTEGER Range(1, None) The number of permutations to be run when computing p-values. [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" /> | |
58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> | |
59 | |
60 </inputs> | |
61 | |
62 <outputs> | |
63 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> | |
64 | |
65 </outputs> | |
66 | |
67 <help><![CDATA[ | |
68 adonis PERMANOVA test for beta group significance | |
69 ############################################################### | |
70 | |
71 Determine whether groups of samples are significantly different from one | |
72 another using the ADONIS permutation-based statistical test in vegan-R. The | |
73 function partitions sums of squares of a multivariate data set, and is | |
74 directly analogous to MANOVA (multivariate analysis of variance). This | |
75 action differs from beta_group_significance in that it accepts R formulae | |
76 to perform multi-way ADONIS tests; beta_group_signficance only performs | |
77 one-way tests. For more details see | |
78 http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html | |
79 | |
80 Parameters | |
81 ---------- | |
82 distance_matrix : DistanceMatrix | |
83 Matrix of distances between pairs of samples. | |
84 metadata : Metadata | |
85 Sample metadata containing formula terms. | |
86 formula : Str | |
87 Model formula containing only independent terms contained in the sample | |
88 metadata. These can be continuous variables or factors, and they can | |
89 have interactions as in a typical R formula. E.g., the formula | |
90 "treatment+block" would test whether the input distance matrix | |
91 partitions based on "treatment" and "block" sample metadata. The | |
92 formula "treatment*block" would test both of those effects as well as | |
93 their interaction. Enclose formulae in quotes to avoid unpleasant | |
94 surprises. | |
95 permutations : Int % Range(1, None), optional | |
96 The number of permutations to be run when computing p-values. | |
97 n_jobs : Int % Range(1, None), optional | |
98 Number of parallel processes to run. | |
99 | |
100 Returns | |
101 ------- | |
102 visualization : Visualization | |
103 ]]></help> | |
104 <macros> | |
105 <import>qiime_citation.xml</import> | |
106 </macros> | |
107 <expand macro="qiime_citation"/> | |
108 </tool> |