|
0
|
1 <?xml version="1.0" ?>
|
|
9
|
2 <tool id="qiime_diversity_bioenv" name="qiime diversity bioenv" version="2019.7">
|
|
0
|
3 <description> - bioenv</description>
|
|
|
4 <requirements>
|
|
9
|
5 <requirement type="package" version="2019.7">qiime2</requirement>
|
|
0
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity bioenv
|
|
|
9
|
|
|
10 --i-distance-matrix=$idistancematrix
|
|
|
11
|
|
|
12
|
|
|
13 #if $input_files_mmetadatafile:
|
|
|
14 #def list_dict_to_string(list_dict):
|
|
|
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
16 #for d in list_dict[1:]:
|
|
|
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
|
18 #end for
|
|
|
19 #return $file_list
|
|
|
20 #end def
|
|
|
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
22 #end if
|
|
|
23
|
|
|
24
|
|
|
25 --o-visualization=ovisualization
|
|
|
26 ;
|
|
|
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
28 && cp -r out/* '$ovisualization.files_path'
|
|
|
29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
30 ]]></command>
|
|
|
31 <inputs>
|
|
|
32 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
|
|
|
33
|
|
4
|
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
|
|
0
|
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
36 </repeat>
|
|
|
37
|
|
|
38 </inputs>
|
|
|
39 <outputs>
|
|
|
40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
41 </outputs>
|
|
|
42 <help><![CDATA[
|
|
|
43 bioenv
|
|
|
44 ######
|
|
|
45
|
|
|
46 Find the subsets of variables in metadata whose Euclidean distances are
|
|
|
47 maximally rank-correlated with distance matrix. All numeric variables in
|
|
|
48 metadata will be considered, and samples which are missing data will be
|
|
|
49 dropped. The output visualization will indicate how many samples were
|
|
|
50 dropped due to missing data, if any were dropped.
|
|
|
51
|
|
|
52 Parameters
|
|
|
53 ----------
|
|
|
54 distance_matrix : DistanceMatrix
|
|
|
55 Matrix of distances between pairs of samples.
|
|
|
56 metadata : Metadata
|
|
|
57 The sample metadata.
|
|
|
58
|
|
|
59 Returns
|
|
|
60 -------
|
|
|
61 visualization : Visualization
|
|
|
62 ]]></help>
|
|
|
63 <macros>
|
|
|
64 <import>qiime_citation.xml</import>
|
|
|
65 </macros>
|
|
|
66 <expand macro="qiime_citation"/>
|
|
|
67 </tool>
|
