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comparison qiime2/qiime_diversity_beta-group-significance.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_beta-group-significance" name="qiime diversity beta-group-significance" version="2018.4">
3 <description> - Beta diversity group significance</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity beta-group-significance --i-distance-matrix=$idistancematrix
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
19
20 #if $ppairwise:
21 --p-pairwise
22 #else
23 --p-no-pairwise
24 #end if
25
26 --o-visualization=ovisualization
27
28 #if str($cmdconfig) != 'None':
29 --cmd-config=$cmdconfig
30 #end if
31
32 #if str($pmethod) != 'None':
33 --p-method=$pmethod
34 #end if
35
36 #if $ppermutations:
37 --p-permutations=$ppermutations
38 #end if
39 ;
40
41 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
42 && cp -r out/* '$ovisualization.files_path'
43 && mv '$ovisualization.files_path/index.html' '$ovisualization';
44 ]]></command>
45 <inputs>
46 <param format="qza,no_unzip.zip" label="--i-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
48 <param 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" format="tabular,qza,no_unzip.zip" />
49 </repeat>
50 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text"/>
51 <param label="--p-method: " name="pmethod" optional="True" type="select">
52 <option selected="True" value="None">Selection is Optional</option>
53 <option value="anosim">anosim</option>
54 <option value="permanova">permanova</option>
55 </param>
56 <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" checked="False" type="boolean"/>
57 <param label="--p-permutations: The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999"/>
58 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
59 </inputs>
60 <outputs>
61 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
62 </outputs>
63 <help><![CDATA[
64 Beta diversity group significance
65 ---------------------------------
66
67 Determine whether groups of samples are significantly different from one
68 another using a permutation-based statistical test.
69
70 Parameters
71 ----------
72 distance_matrix : DistanceMatrix
73 Matrix of distances between pairs of samples.
74 metadata : MetadataColumn[Categorical]
75 Categorical sample metadata column.
76 method : Str % Choices({'anosim', 'permanova'}), optional
77 The group significance test to be applied.
78 pairwise : Bool, optional
79 Perform pairwise tests between all pairs of groups in addition to the
80 test across all groups. This can be very slow if there are a lot of
81 groups in the metadata column.
82 permutations : Int, optional
83 The number of permutations to be run when computing p-values.
84
85 Returns
86 -------
87 visualization : Visualization
88 \
89 ]]>
90 </help>
91 <macros>
92 <import>qiime_citation.xml</import>
93 </macros>
94 <expand macro="qiime_citation" />
95 </tool>