|
20
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance"
|
|
|
3 version="2020.8">
|
|
|
4 <description>Alpha diversity comparisons</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime diversity alpha-group-significance
|
|
|
10
|
|
|
11 --i-alpha-diversity=$ialphadiversity
|
|
|
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($input_files_mmetadatafile)
|
|
|
21 # end if
|
|
|
22
|
|
|
23 --o-visualization=ovisualization
|
|
|
24
|
|
|
25 #if str($examples) != 'None':
|
|
|
26 --examples=$examples
|
|
|
27 #end if
|
|
|
28
|
|
|
29 ;
|
|
|
30 cp oalphadiversity.qza $oalphadiversity
|
|
|
31
|
|
|
32 ;
|
|
|
33 qiime tools export ovisualization.qzv --output-path out
|
|
|
34 && mkdir -p '$ovisualization.files_path'
|
|
|
35 && cp -r out/* '$ovisualization.files_path'
|
|
|
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
37
|
|
|
38 ;
|
|
|
39 qiime tools export ovisualization.qzv --output-path out
|
|
|
40 && mkdir -p '$ovisualization.files_path'
|
|
|
41 && cp -r out/* '$ovisualization.files_path'
|
|
|
42 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
43
|
|
|
44 ]]></command>
|
|
|
45 <inputs>
|
|
|
46 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" />
|
|
|
47 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
48 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
|
|
|
49 </repeat>
|
|
|
50 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
51
|
|
|
52 </inputs>
|
|
|
53
|
|
|
54 <outputs>
|
|
|
55 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
|
|
|
56
|
|
|
57 </outputs>
|
|
|
58
|
|
|
59 <help><![CDATA[
|
|
|
60 Alpha diversity comparisons
|
|
|
61 ###############################################################
|
|
|
62
|
|
|
63 Visually and statistically compare groups of alpha diversity values.
|
|
|
64
|
|
|
65 Parameters
|
|
|
66 ----------
|
|
|
67 alpha_diversity : SampleData[AlphaDiversity]
|
|
|
68 Vector of alpha diversity values by sample.
|
|
|
69 metadata : Metadata
|
|
|
70 The sample metadata.
|
|
|
71
|
|
|
72 Returns
|
|
|
73 -------
|
|
|
74 visualization : Visualization
|
|
|
75 ]]></help>
|
|
|
76 <macros>
|
|
|
77 <import>qiime_citation.xml</import>
|
|
|
78 </macros>
|
|
|
79 <expand macro="qiime_citation"/>
|
|
|
80 </tool> |
