Mercurial > repos > florianbegusch > qiime2_suite_zmf
comparison qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml @ 0:5c352d975ef7 draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:33:04 +0000 |
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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> |