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comparison qiime2-2020.8/qiime_diversity_alpha-correlation.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation"
3 version="2020.8">
4 <description>Alpha diversity correlation</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime diversity alpha-correlation
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($input_files_mmetadatafile)
21 # end if
22
23 #if str($pmethod) != 'None':
24 --p-method=$pmethod
25 #end if
26
27 #if $pintersectids:
28 --p-intersect-ids
29 #end if
30
31 --o-visualization=ovisualization
32
33 #if str($examples) != 'None':
34 --examples=$examples
35 #end if
36
37 ;
38 cp oalphadiversity.qza $oalphadiversity
39
40 ;
41 qiime tools export ovisualization.qzv --output-path out
42 && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
45
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data" />
49 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
50 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [required]" name="additional_input" optional="False" type="data" />
51 </repeat>
52 <param label="--p-method: " name="pmethod" optional="True" type="select">
53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="spearman">spearman</option>
55 <option value="pearson">pearson</option>
56 </param>
57 <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" />
58 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
59
60 </inputs>
61
62 <outputs>
63 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
64
65 </outputs>
66
67 <help><![CDATA[
68 Alpha diversity correlation
69 ###############################################################
70
71 Determine whether numeric sample metadata columns are correlated with alpha
72 diversity.
73
74 Parameters
75 ----------
76 alpha_diversity : SampleData[AlphaDiversity]
77 Vector of alpha diversity values by sample.
78 metadata : Metadata
79 The sample metadata.
80 method : Str % Choices('spearman', 'pearson'), optional
81 The correlation test to be applied.
82 intersect_ids : Bool, optional
83 If supplied, IDs that are not found in both the alpha diversity vector
84 and metadata will be discarded before calculating the correlation.
85 Default behavior is to error on any mismatched IDs.
86
87 Returns
88 -------
89 visualization : Visualization
90 ]]></help>
91 <macros>
92 <import>qiime_citation.xml</import>
93 </macros>
94 <expand macro="qiime_citation"/>
95 </tool>