|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2019.4">
|
|
|
3 <description> - Alpha diversity correlation</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity alpha-correlation
|
|
|
9
|
|
|
10 --i-alpha-diversity=$ialphadiversity
|
|
|
11
|
|
|
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($input_files_mmetadatafile)
|
|
|
21 #end if
|
|
|
22
|
|
|
23 #if str($pmethod) != 'None':
|
|
|
24 --p-method=$pmethod
|
|
|
25 #end if
|
|
|
26
|
|
|
27 --o-visualization=ovisualization
|
|
|
28 ;
|
|
|
29 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
30 && cp -r out/* '$ovisualization.files_path'
|
|
|
31 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
32 ]]></command>
|
|
|
33 <inputs>
|
|
|
34 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
|
|
|
35 <param label="--p-method: " name="pmethod" optional="True" type="select">
|
|
|
36 <option selected="True" value="None">Selection is Optional</option>
|
|
|
37 <option value="spearman">spearman</option>
|
|
|
38 <option value="pearson">pearson</option>
|
|
|
39 </param>
|
|
|
40
|
|
|
41 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
|
|
|
42 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
43 </repeat>
|
|
|
44 </inputs>
|
|
|
45 <outputs>
|
|
|
46 <data format="qza" label="${tool.name} on ${on_string}: metadatafile.qza" name="mmetadatafile"/>
|
|
|
47 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
48 </outputs>
|
|
|
49 <help><![CDATA[
|
|
|
50 Alpha diversity correlation
|
|
|
51 ###########################
|
|
|
52
|
|
|
53 Determine whether numeric sample metadata columns are correlated with alpha
|
|
|
54 diversity.
|
|
|
55
|
|
|
56 Parameters
|
|
|
57 ----------
|
|
|
58 alpha_diversity : SampleData[AlphaDiversity]
|
|
|
59 Vector of alpha diversity values by sample.
|
|
|
60 metadata : Metadata
|
|
|
61 The sample metadata.
|
|
|
62 method : Str % Choices('spearman', 'pearson'), optional
|
|
|
63 The correlation test to be applied.
|
|
|
64
|
|
|
65 Returns
|
|
|
66 -------
|
|
|
67 visualization : Visualization
|
|
|
68 ]]></help>
|
|
|
69 <macros>
|
|
|
70 <import>qiime_citation.xml</import>
|
|
|
71 </macros>
|
|
|
72 <expand macro="qiime_citation"/>
|
|
|
73 </tool>
|
