|
2
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.4">
|
|
|
3 <description> - Summarize table</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime feature-table summarize
|
|
|
9
|
|
|
10 --i-table=$itable
|
|
|
11
|
|
4
|
12
|
|
|
13 #if $m_sample_metadatafile:
|
|
2
|
14 #def list_dict_to_string(list_dict):
|
|
|
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
|
16 #for d in list_dict[1:]:
|
|
|
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
|
18 #end for
|
|
|
19 #return $file_list
|
|
|
20 #end def
|
|
|
21 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
|
|
4
|
22 #end if
|
|
|
23
|
|
2
|
24
|
|
|
25 --o-visualization=ovisualization
|
|
|
26 ;
|
|
|
27 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
|
|
|
28 && cp -r out/* '$ovisualization.files_path'
|
|
|
29 && mv '$ovisualization.files_path/index.html' '$ovisualization'
|
|
|
30 ]]></command>
|
|
|
31 <inputs>
|
|
|
32 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
|
|
|
33
|
|
|
34 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
|
|
|
35 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
|
36 </repeat>
|
|
|
37 </inputs>
|
|
|
38 <outputs>
|
|
|
39 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
|
|
|
40 </outputs>
|
|
|
41 <help><![CDATA[
|
|
|
42 Summarize table
|
|
|
43 ###############
|
|
|
44
|
|
|
45 Generate visual and tabular summaries of a feature table.
|
|
|
46
|
|
|
47 Parameters
|
|
|
48 ----------
|
|
|
49 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
|
|
|
50 The feature table to be summarized.
|
|
|
51 sample_metadata : Metadata, optional
|
|
|
52 The sample metadata.
|
|
|
53
|
|
|
54 Returns
|
|
|
55 -------
|
|
|
56 visualization : Visualization
|
|
|
57 ]]></help>
|
|
|
58 <macros>
|
|
|
59 <import>qiime_citation.xml</import>
|
|
|
60 </macros>
|
|
|
61 <expand macro="qiime_citation"/>
|
|
|
62 </tool>
|
