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comparison qiime2/qiime_feature-table_summarize.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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children 51025741f326
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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
12 #def list_dict_to_string(list_dict):
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 #for d in list_dict[1:]:
15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
16 #end for
17 #return $file_list
18 #end def
19 --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
20
21 --o-visualization=ovisualization
22 ;
23 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
24 && cp -r out/* '$ovisualization.files_path'
25 && mv '$ovisualization.files_path/index.html' '$ovisualization'
26 ]]></command>
27 <inputs>
28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
29
30 <repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
31 <param label="--m-sample-metadata-file: (multiple arguments will be merged) The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
32 </repeat>
33 </inputs>
34 <outputs>
35 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
36 </outputs>
37 <help><![CDATA[
38 Summarize table
39 ###############
40
41 Generate visual and tabular summaries of a feature table.
42
43 Parameters
44 ----------
45 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
46 The feature table to be summarized.
47 sample_metadata : Metadata, optional
48 The sample metadata.
49
50 Returns
51 -------
52 visualization : Visualization
53 ]]></help>
54 <macros>
55 <import>qiime_citation.xml</import>
56 </macros>
57 <expand macro="qiime_citation"/>
58 </tool>