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comparison qiime2/qiime_diversity_beta-group-significance.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance"
3 version="2020.8">
4 <description>Beta diversity group significance</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity beta-group-significance
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($input_files_mmetadatafile)
21 # end if
22
23 #if '__ob__' in str($mmetadatacolumn):
24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
25 #set $mmetadatacolumn = $mmetadatacolumn_temp
26 #end if
27 #if '__cb__' in str($mmetadatacolumn):
28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
29 #set $mmetadatacolumn = $mmetadatacolumn_temp
30 #end if
31 #if 'X' in str($mmetadatacolumn):
32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
33 #set $mmetadatacolumn = $mmetadatacolumn_temp
34 #end if
35 #if '__sq__' in str($mmetadatacolumn):
36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
37 #set $mmetadatacolumn = $mmetadatacolumn_temp
38 #end if
39 #if '__db__' in str($mmetadatacolumn):
40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
41 #set $mmetadatacolumn = $mmetadatacolumn_temp
42 #end if
43
44 --m-metadata-column=$mmetadatacolumn
45
46
47 #if str($pmethod) != 'None':
48 --p-method=$pmethod
49 #end if
50
51 #if $ppairwise:
52 --p-pairwise
53 #end if
54
55 --p-permutations=$ppermutations
56
57 --o-visualization=ovisualization
58
59 #if str($examples) != 'None':
60 --examples=$examples
61 #end if
62
63 ;
64 cp odistancematrix.qza $odistancematrix
65
66 ;
67 qiime tools export omantelscattervisualization.qzv --output-path out
68 && mkdir -p '$omantelscattervisualization.files_path'
69 && cp -r out/* '$omantelscattervisualization.files_path'
70 && mv '$omantelscattervisualization.files_path/index.html' '$omantelscattervisualization'
71
72 ;
73 qiime tools export ovisualization.qzv --output-path out
74 && mkdir -p '$ovisualization.files_path'
75 && cp -r out/* '$ovisualization.files_path'
76 && mv '$ovisualization.files_path/index.html' '$ovisualization'
77
78 ]]></command>
79 <inputs>
80 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
81 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
82 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
83 </repeat>
84 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical sample metadata column. [required]" name="mmetadatacolumn" optional="False" type="text" />
85 <param label="--p-method: " name="pmethod" optional="True" type="select">
86 <option selected="True" value="None">Selection is Optional</option>
87 <option value="permanova">permanova</option>
88 <option value="anosim">anosim</option>
89 <option value="permdisp">permdisp</option>
90 </param>
91 <param label="--p-pairwise: --p-pairwise: / --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column. [default: False]" name="ppairwise" selected="False" type="boolean" />
92 <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values. [default: 999]" name="ppermutations" optional="True" type="integer" value="999" />
93 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
94
95 </inputs>
96
97 <outputs>
98 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
99
100 </outputs>
101
102 <help><![CDATA[
103 Beta diversity group significance
104 ###############################################################
105
106 Determine whether groups of samples are significantly different from one
107 another using a permutation-based statistical test.
108
109 Parameters
110 ----------
111 distance_matrix : DistanceMatrix
112 Matrix of distances between pairs of samples.
113 metadata : MetadataColumn[Categorical]
114 Categorical sample metadata column.
115 method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
116 The group significance test to be applied.
117 pairwise : Bool, optional
118 Perform pairwise tests between all pairs of groups in addition to the
119 test across all groups. This can be very slow if there are a lot of
120 groups in the metadata column.
121 permutations : Int, optional
122 The number of permutations to be run when computing p-values.
123
124 Returns
125 -------
126 visualization : Visualization
127 ]]></help>
128 <macros>
129 <import>qiime_citation.xml</import>
130 </macros>
131 <expand macro="qiime_citation"/>
132 </tool>