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comparison qiime2/qiime_diversity_alpha-correlation.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_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>