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comparison qiime2/qiime_metadata_tabulate.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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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2019.4">
3 <description> - Interactively explore Metadata in an HTML table</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime metadata tabulate
9
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ' --m-input-file=' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18 --m-input-file=$list_dict_to_string($input_files_minputfile)
19
20
21 #if $ppagesize:
22 --p-page-size=$ppagesize
23 #end if
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 label="--p-page-size: INTEGER The maximum number of Metadata records to display per page [default: 100]" name="ppagesize" optional="True" type="integer" value="100"/>
33
34 <repeat name="input_files_minputfile" optional="False" title="--m-input-file">
35 <param label="--m-input-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The metadata to tabulate. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
36 </repeat>
37
38 </inputs>
39 <outputs>
40 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
41 </outputs>
42 <help><![CDATA[
43 Interactively explore Metadata in an HTML table
44 ###############################################
45
46 Generate a tabular view of Metadata. The output visualization supports
47 interactive filtering, sorting, and exporting to common file formats.
48
49 Parameters
50 ----------
51 input : Metadata
52 The metadata to tabulate.
53 page_size : Int, optional
54 The maximum number of Metadata records to display per page
55
56 Returns
57 -------
58 visualization : Visualization
59 ]]></help>
60 <macros>
61 <import>qiime_citation.xml</import>
62 </macros>
63 <expand macro="qiime_citation"/>
64 </tool>