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comparison qiime2-2020.8/qiime_demux_summarize.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_summarize" name="qiime demux summarize"
3 version="2020.8">
4 <description>Summarize counts per sample.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime demux summarize
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($input_files_idata)
19 # end if
20
21 --p-n=$pn
22
23 --o-visualization=ovisualization
24
25 #if str($examples) != 'None':
26 --examples=$examples
27 #end if
28
29 ;
30 cp osubsampledsequences.qza $osubsampledsequences
31
32 ;
33 qiime tools export ovisualization.qzv --output-path out
34 && mkdir -p '$ovisualization.files_path'
35 && cp -r out/* '$ovisualization.files_path'
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37
38 ]]></command>
39 <inputs>
40 <repeat name="input_files_idata" optional="False" title="--i-data">
41 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="additional_input" optional="False" type="data" />
42 </repeat>
43 <param label="--p-n: INTEGER The number of sequences that should be selected at random for quality score plots. The quality plots will present the average positional qualities across all of the sequences selected. If input sequences are paired end, plots will be generated for both forward and reverse reads for the same `n` sequences. [default: 10000]" name="pn" optional="True" type="integer" value="10000" />
44 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
45
46 </inputs>
47
48 <outputs>
49 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
50
51 </outputs>
52
53 <help><![CDATA[
54 Summarize counts per sample.
55 ###############################################################
56
57 Summarize counts per sample for all samples, and generate interactive
58 positional quality plots based on `n` randomly selected sequences.
59
60 Parameters
61 ----------
62 data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
63 The demultiplexed sequences to be summarized.
64 n : Int, optional
65 The number of sequences that should be selected at random for quality
66 score plots. The quality plots will present the average positional
67 qualities across all of the sequences selected. If input sequences are
68 paired end, plots will be generated for both forward and reverse reads
69 for the same `n` sequences.
70
71 Returns
72 -------
73 visualization : Visualization
74 ]]></help>
75 <macros>
76 <import>qiime_citation.xml</import>
77 </macros>
78 <expand macro="qiime_citation"/>
79 </tool>