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comparison qiime_diversity_alpha-correlation.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation" version="2018.4">
3 <description> - Alpha diversity correlation</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime diversity alpha-correlation
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-alpha-diversity=$ialphadiversity
19
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 #if str($pmethod) != 'None':
25 --p-method=$pmethod
26 #end if
27
28 --o-visualization=ovisualization;
29
30 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
31 && cp -r out/* '$ovisualization.files_path'
32 && mv '$ovisualization.files_path/index.html' '$ovisualization';
33 ]]></command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-alpha-diversity: SampleData[AlphaDiversity] Vector of alpha diversity values by sample. [required]" name="ialphadiversity" optional="False" type="data"/>
36 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
37 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
38 </repeat>
39 <param label="--p-method: " name="pmethod" optional="True" type="select" >
40 <option selected="True" value="None">Selection is Optional</option>
41 <option value="spearman">spearman</option>
42 <option value="pearson">pearson</option>
43 </param>
44 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
45 </inputs>
46 <outputs>
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({'pearson', 'spearman'}), optional
63 The correlation test to be applied.
64
65 Returns
66 -------
67 visualization : Visualization
68 \
69 ]]>
70 </help>
71 </tool>