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comparison qiime2-2020.8/qiime_diversity_alpha-group-significance.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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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>