Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_diversity_alpha-correlation.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | 914fa4daf16a |
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-1:000000000000 | 0:370e0b6e9826 |
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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> |