Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_diversity_bioenv.xml @ 0:370e0b6e9826 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children 914fa4daf16a
comparison
equal deleted inserted replaced
-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_bioenv" name="qiime diversity bioenv" version="2019.4">
3 <description> - bioenv</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
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 cp mmetadatafile.qza $mmetadatafile;
28 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
29 && cp -r out/* '$ovisualization.files_path'
30 && mv '$ovisualization.files_path/index.html' '$ovisualization';
31 ]]></command>
32 <inputs>
33 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
34
35 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
36 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
37 </repeat>
38
39 </inputs>
40 <outputs>
41 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
42 </outputs>
43 <help><![CDATA[
44 bioenv
45 ######
46
47 Find the subsets of variables in metadata whose Euclidean distances are
48 maximally rank-correlated with distance matrix. All numeric variables in
49 metadata will be considered, and samples which are missing data will be
50 dropped. The output visualization will indicate how many samples were
51 dropped due to missing data, if any were dropped.
52
53 Parameters
54 ----------
55 distance_matrix : DistanceMatrix
56 Matrix of distances between pairs of samples.
57 metadata : Metadata
58 The sample metadata.
59
60 Returns
61 -------
62 visualization : Visualization
63 ]]></help>
64 <macros>
65 <import>qiime_citation.xml</import>
66 </macros>
67 <expand macro="qiime_citation"/>
68 </tool>