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comparison qiime2-2020.8/qiime_feature-table_summarize.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_feature-table_summarize" name="qiime feature-table summarize"
3 version="2020.8">
4 <description>Summarize table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table summarize
10
11 --i-table=$itable
12 # if $input_files_msamplemetadatafile:
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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
21 # end if
22
23 --o-visualization=ovisualization
24
25 #if str($examples) != 'None':
26 --examples=$examples
27 #end if
28
29 ;
30 cp osampledtable.qza $osampledtable
31
32 ;
33 qiime tools export ovisualization.qzv --output-path out
34 && mkdir -p '$ovisualization.files_path'
35 && cp -r out/* '$ovisualization.files_path'
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37
38 ]]></command>
39 <inputs>
40 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] The feature table to be summarized. [required]" name="itable" optional="False" type="data" />
41 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
42 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple The sample metadata. arguments will be merged) [optional]" name="additional_input" optional="True" type="data" />
43 </repeat>
44 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
45
46 </inputs>
47
48 <outputs>
49 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
50
51 </outputs>
52
53 <help><![CDATA[
54 Summarize table
55 ###############################################################
56
57 Generate visual and tabular summaries of a feature table.
58
59 Parameters
60 ----------
61 table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
62 The feature table to be summarized.
63 sample_metadata : Metadata, optional
64 The sample metadata.
65
66 Returns
67 -------
68 visualization : Visualization
69 ]]></help>
70 <macros>
71 <import>qiime_citation.xml</import>
72 </macros>
73 <expand macro="qiime_citation"/>
74 </tool>