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comparison qiime2/qiime_metadata_tabulate.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2018.4">
3 <description> - Interactively explore Metadata in an HTML table</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime metadata tabulate
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 $file_list
17 #end def
18
19 --m-input-file=$list_dict_to_string($input_files_minputfile)
20 #if str($cmdconfig) != 'None':
21 --cmd-config=$cmdconfig
22 #end if
23
24 #if $ppagesize:
25 --p-page-size=$ppagesize
26 #end if
27 --o-visualization=ovisualization;
28 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
29 && cp -r out/* '$ovisualization.files_path'
30 && mv '$ovisualization.files_path/index.html' '$ovisualization'
31 ]]>
32 </command>
33 <inputs>
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 <param label="--p-page-size: The maximum number of Metadata records to display per page [default: 100]" name="ppagesize" optional="True" type="integer" value="100"/>
39
40 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
41 </inputs>
42 <outputs>
43 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
44 </outputs>
45 <help>
46 <![CDATA[
47 Interactively explore Metadata in an HTML table
48 ------------------------------------------------
49
50 Generate a tabular view of Metadata. The output visualization supports
51 interactive filtering, sorting, and exporting to common file formats.
52
53 Parameters
54 ----------
55 input : Metadata
56 The metadata to tabulate.
57 page_size : Int, optional
58 The maximum number of Metadata records to display per page
59
60 Returns
61 -------
62 visualization : Visualization
63 \
64 ]]>
65 </help>
66 <macros>
67 <import>qiime_citation.xml</import>
68 </macros>
69 <expand macro="qiime_citation" />
70 </tool>