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comparison qiime2/qiime_diversity_beta-group-significance.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_beta-group-significance" name="qiime diversity beta-group-significance" version="2019.4">
3 <description> - Beta diversity group significance</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-group-significance
9
10 --i-distance-matrix=$idistancematrix
11 --m-metadata-column="$mmetadatacolumn"
12
13
14
15 #if $input_files_mmetadatafile:
16 #def list_dict_to_string(list_dict):
17 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
18 #for d in list_dict[1:]:
19 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
20 #end for
21 #return $file_list
22 #end def
23 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
24 #end if
25
26
27
28 #if str($pmethod) != 'None':
29 --p-method=$pmethod
30 #end if
31
32 #if $ppairwise:
33 --p-pairwise
34 #end if
35
36 #if $ppermutations:
37 --p-permutations=$ppermutations
38 #end if
39
40 --o-visualization=ovisualization
41 ;
42 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
45 ]]></command>
46 <inputs>
47 <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"/>
48 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text"/>
49 <param label="--p-method: " name="pmethod" optional="True" type="select">
50 <option selected="True" value="None">Selection is Optional</option>
51 <option value="permanova">permanova</option>
52 <option value="anosim">anosim</option>
53 <option value="permdisp">permdisp</option>
54 </param>
55 <param label="--p-pairwise: --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" selected="False" type="boolean"/>
56 <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
57
58 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
59 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
60 </repeat>
61 </inputs>
62 <outputs>
63 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
64 </outputs>
65 <help><![CDATA[
66 Beta diversity group significance
67 #################################
68
69 Determine whether groups of samples are significantly different from one
70 another using a permutation-based statistical test.
71
72 Parameters
73 ----------
74 distance_matrix : DistanceMatrix
75 Matrix of distances between pairs of samples.
76 metadata : MetadataColumn[Categorical]
77 Categorical sample metadata column.
78 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
79 The group significance test to be applied.
80 pairwise : Bool, optional
81 Perform pairwise tests between all pairs of groups in addition to the
82 test across all groups. This can be very slow if there are a lot of
83 groups in the metadata column.
84 permutations : Int, optional
85 The number of permutations to be run when computing p-values.
86
87 Returns
88 -------
89 visualization : Visualization
90 ]]></help>
91 <macros>
92 <import>qiime_citation.xml</import>
93 </macros>
94 <expand macro="qiime_citation"/>
95 </tool>