annotate qiime2/qiime_diversity_bioenv.xml @ 10:21c7954105a9 draft

Fix
author florianbegusch
date Sun, 25 Aug 2019 10:26:27 -0400
parents f190567fe3f6
children a0a8d77a991c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
2 <tool id="qiime_diversity_bioenv" name="qiime diversity bioenv" version="2019.7">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - bioenv</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
9
f190567fe3f6 Uploaded
florianbegusch
parents: 4
diff changeset
5 <requirement type="package" version="2019.7">qiime2</requirement>
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime diversity bioenv
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-distance-matrix=$idistancematrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 #if $input_files_mmetadatafile:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #def list_dict_to_string(list_dict):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #for d in list_dict[1:]:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #end for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #return $file_list
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end def
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33
4
florianbegusch
parents: 0
diff changeset
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 </repeat>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 bioenv
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 ######
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 Find the subsets of variables in metadata whose Euclidean distances are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 maximally rank-correlated with distance matrix. All numeric variables in
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 metadata will be considered, and samples which are missing data will be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 dropped. The output visualization will indicate how many samples were
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 dropped due to missing data, if any were dropped.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 distance_matrix : DistanceMatrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 Matrix of distances between pairs of samples.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 metadata : Metadata
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 The sample metadata.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 </tool>