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comparison qiime2/qiime_metadata_distance-matrix.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_metadata_distance-matrix" name="qiime metadata distance-matrix" version="2019.4">
3 <description> - Create a distance matrix from a numeric Metadata column</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime metadata distance-matrix
9
10 --m-metadata-column="$mmetadatacolumn"
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-distance-matrix=odistancematrix
26 ;
27 cp odistancematrix.qza $odistancematrix
28 ]]></command>
29 <inputs>
30 <param label="--m-metadata-column: COLUMN MetadataColumn[Numeric] Numeric metadata column to compute pairwise Euclidean distances from [required]" name="mmetadatacolumn" optional="False" type="text"/>
31
32 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
33 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
34 </repeat>
35
36 </inputs>
37 <outputs>
38 <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
39 </outputs>
40 <help><![CDATA[
41 Create a distance matrix from a numeric Metadata column
42 #######################################################
43
44 Create a distance matrix from a numeric metadata column. The Euclidean
45 distance is computed between each pair of samples or features in the
46 column. Tip: the distance matrix produced by this method can be used as
47 input to the Mantel test available in `q2-diversity`.
48
49 Parameters
50 ----------
51 metadata : MetadataColumn[Numeric]
52 Numeric metadata column to compute pairwise Euclidean distances from
53
54 Returns
55 -------
56 distance_matrix : DistanceMatrix
57 ]]></help>
58 <macros>
59 <import>qiime_citation.xml</import>
60 </macros>
61 <expand macro="qiime_citation"/>
62 </tool>