|
20
|
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> |
