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comparison qiime2/qiime_diversity_bioenv.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_bioenv" name="qiime diversity bioenv" version="2018.4">
3 <description> - bioenv</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime diversity bioenv --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($input_files_mmetadatafile)
19
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 --o-visualization=ovisualization;
25 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
26 && cp -r out/* '$ovisualization.files_path'
27 && mv '$ovisualization.files_path/index.html' '$ovisualization';
28 ]]></command>
29 <inputs>
30 <param format="qza,no_unzip.zip" label="--i-distance-matrix: DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
31 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
32 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
33 </repeat>
34 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
35 </inputs>
36 <outputs>
37 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
38 </outputs>
39 <help>
40 <![CDATA[
41 bioenv
42 ------
43
44 Find the subsets of variables in metadata whose Euclidean distances are
45 maximally rank-correlated with distance matrix. All numeric variables in
46 metadata will be considered, and samples which are missing data will be
47 dropped. The output visualization will indicate how many samples were
48 dropped due to missing data, if any were dropped.
49
50 Parameters
51 ----------
52 distance_matrix : DistanceMatrix
53 Matrix of distances between pairs of samples.
54 metadata : Metadata
55 The sample metadata.
56
57 Returns
58 -------
59 visualization : Visualization
60 \
61 ]]>
62 </help>
63 <macros>
64 <import>qiime_citation.xml</import>
65 </macros>
66 <expand macro="qiime_citation" />
67 </tool>