|
2
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2019.4">
|
|
|
3 <description> - Alpha diversity comparisons</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity alpha-group-significance
|
|
|
9
|
|
|
10 --i-alpha-diversity=$ialphadiversity
|
|
|
11
|
|
|
12
|
|
4
|
13 #if $input_files_mmetadatafile:
|
|
2
|
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:]:
|
|
4
|
17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
|
|
2
|
18 #end for
|
|
|
19 #return $file_list
|
|
|
20 #end def
|
|
4
|
21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
|
|
|
22 #end if
|
|
2
|
23
|
|
|
24
|
|
|
25 --o-visualization=ovisualization
|
|
|
26 ;
|
|
|
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
28 && cp -r out/* '$ovisualization.files_path'
|
|
|
29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
30 ]]></command>
|
|
|
31 <inputs>
|
|
|
32 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
|
|
|
33
|
|
4
|
34 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file [required]">
|
|
2
|
35 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
36 </repeat>
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
40 </outputs>
|
|
|
41 <help><![CDATA[
|
|
4
|
42 Alpha diversity comparisons
|
|
2
|
43
|
|
4
|
44 Visually and statistically compare groups of alpha diversity values.
|
|
2
|
45
|
|
|
46 Parameters
|
|
|
47 ----------
|
|
4
|
48 alpha_diversity : SampleData[AlphaDiversity]
|
|
|
49 Vector of alpha diversity values by sample.
|
|
|
50 metadata : Metadata
|
|
|
51 The sample metadata.
|
|
2
|
52
|
|
|
53 Returns
|
|
|
54 -------
|
|
|
55 visualization : Visualization
|
|
|
56 ]]></help>
|
|
|
57 <macros>
|
|
|
58 <import>qiime_citation.xml</import>
|
|
|
59 </macros>
|
|
|
60 <expand macro="qiime_citation"/>
|
|
|
61 </tool>
|
