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comparison qiime2/qiime_diversity_bioenv.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_bioenv" name="qiime diversity bioenv"
3 version="2020.8">
4 <description>bioenv</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity bioenv
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($input_files_mmetadatafile)
21 # end if
22
23 --o-visualization=ovisualization
24
25 #if str($examples) != 'None':
26 --examples=$examples
27 #end if
28
29 ;
30 cp odistancematrix.qza $odistancematrix
31
32 ;
33 qiime tools export ovisualization.qzv --output-path out
34 && mkdir -p '$ovisualization.files_path'
35 && cp -r out/* '$ovisualization.files_path'
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37
38 ;
39 qiime tools export ovisualization.qzv --output-path out
40 && mkdir -p '$ovisualization.files_path'
41 && cp -r out/* '$ovisualization.files_path'
42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
43
44 ]]></command>
45 <inputs>
46 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
48 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
49 </repeat>
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
51
52 </inputs>
53
54 <outputs>
55 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
56
57 </outputs>
58
59 <help><![CDATA[
60 bioenv
61 ###############################################################
62
63 Find the subsets of variables in metadata whose Euclidean distances are
64 maximally rank-correlated with distance matrix. All numeric variables in
65 metadata will be considered, and samples which are missing data will be
66 dropped. The output visualization will indicate how many samples were
67 dropped due to missing data, if any were dropped.
68
69 Parameters
70 ----------
71 distance_matrix : DistanceMatrix
72 Matrix of distances between pairs of samples.
73 metadata : Metadata
74 The sample metadata.
75
76 Returns
77 -------
78 visualization : Visualization
79 ]]></help>
80 <macros>
81 <import>qiime_citation.xml</import>
82 </macros>
83 <expand macro="qiime_citation"/>
84 </tool>