|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_diversity_alpha-group-significance" name="qiime diversity alpha-group-significance" version="2018.4">
|
|
|
3 <description> - Alpha diversity comparisons</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime diversity alpha-group-significance
|
|
|
9 #def list_dict_to_string(list_dict):
|
|
|
10 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
11 #for d in list_dict[1:]:
|
|
|
12 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
|
13 #end for
|
|
|
14 #return $file_list
|
|
|
15 #end def
|
|
|
16
|
|
|
17 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-alpha-diversity=$ialphadiversity
|
|
|
18
|
|
|
19 #if str($cmdconfig) != 'None':
|
|
|
20 --cmd-config=$cmdconfig
|
|
|
21 #end if
|
|
|
22
|
|
|
23 --o-visualization=ovisualization;
|
|
|
24 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
|
|
|
25 && cp -r out/* '$ovisualization.files_path'
|
|
|
26 && mv '$ovisualization.files_path/index.html' '$ovisualization';
|
|
|
27 ]]></command>
|
|
|
28 <inputs>
|
|
|
29 <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"/>
|
|
|
30 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
|
|
|
31 <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" />
|
|
|
32 </repeat>
|
|
|
33 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
34 </inputs>
|
|
|
35 <outputs>
|
|
|
36 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
37 </outputs>
|
|
|
38 <help><![CDATA[
|
|
|
39 Alpha diversity comparisons
|
|
|
40 ----------------------------
|
|
|
41
|
|
|
42 Visually and statistically compare groups of alpha diversity values.
|
|
|
43
|
|
|
44 Parameters
|
|
|
45 ----------
|
|
|
46 alpha_diversity : SampleData[AlphaDiversity]
|
|
|
47 Vector of alpha diversity values by sample.
|
|
|
48 metadata : Metadata
|
|
|
49 The sample metadata.
|
|
|
50
|
|
|
51 Returns
|
|
|
52 -------
|
|
|
53 visualization : Visualization
|
|
|
54 \
|
|
|
55 ]]>
|
|
|
56 </help>
|
|
|
57 </tool>
|
