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comparison qiime2-2020.8/qiime_feature-table_tabulate-seqs.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_tabulate-seqs" name="qiime feature-table tabulate-seqs"
3 version="2020.8">
4 <description>View sequence associated with each feature</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table tabulate-seqs
10 # if $input_files_idata:
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 + ' --i-data=' + d['additional_input'].__getattr__('file_name')
15 # end for
16 # return $file_list
17 # end def
18 --i-data=$list_dict_to_string($input_files_idata)
19 # end if
20
21 --o-visualization=ovisualization
22
23 #if str($examples) != 'None':
24 --examples=$examples
25 #end if
26
27 ;
28 cp osampledtable.qza $osampledtable
29
30 ;
31 qiime tools export ovisualization.qzv --output-path out
32 && mkdir -p '$ovisualization.files_path'
33 && cp -r out/* '$ovisualization.files_path'
34 && mv '$ovisualization.files_path/index.html' '$ovisualization'
35
36 ;
37 qiime tools export ovisualization.qzv --output-path out
38 && mkdir -p '$ovisualization.files_path'
39 && cp -r out/* '$ovisualization.files_path'
40 && mv '$ovisualization.files_path/index.html' '$ovisualization'
41
42 ]]></command>
43 <inputs>
44 <repeat name="input_files_idata" optional="False" title="--i-data">
45 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated. [required]" name="additional_input" optional="False" type="data" />
46 </repeat>
47 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
48
49 </inputs>
50
51 <outputs>
52 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
53
54 </outputs>
55
56 <help><![CDATA[
57 View sequence associated with each feature
58 ###############################################################
59
60 Generate tabular view of feature identifier to sequence mapping, including
61 links to BLAST each sequence against the NCBI nt database.
62
63 Parameters
64 ----------
65 data : FeatureData[Sequence | AlignedSequence]
66 The feature sequences to be tabulated.
67
68 Returns
69 -------
70 visualization : Visualization
71 ]]></help>
72 <macros>
73 <import>qiime_citation.xml</import>
74 </macros>
75 <expand macro="qiime_citation"/>
76 </tool>