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comparison qiime2-2020.8/qiime_vsearch_fastq-stats.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_vsearch_fastq-stats" name="qiime vsearch fastq-stats"
3 version="2020.8">
4 <description>Fastq stats with vsearch.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime vsearch fastq-stats
10
11 --i-sequences=$isequences
12
13 #if str($pthreads) != 'None':
14 --p-threads=$pthreads
15 #end if
16
17 --o-visualization=ovisualization
18
19 #if str($examples) != 'None':
20 --examples=$examples
21 #end if
22
23 ;
24 cp odereplicatedsequences.qza $odereplicatedsequences
25
26 ;
27 qiime tools export ovisualization.qzv --output-path out
28 && mkdir -p '$ovisualization.files_path'
29 && cp -r out/* '$ovisualization.files_path'
30 && mv '$ovisualization.files_path/index.html' '$ovisualization'
31
32 ]]></command>
33 <inputs>
34 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] Fastq sequences [required]" name="isequences" optional="False" type="data" />
35 <param label="--p-threads: " name="pthreads" optional="True" type="select">
36 <option selected="True" value="None">Selection is Optional</option>
37 <option value="Int % Range(1">Int % Range(1</option>
38 <option value="None">None</option>
39 </param>
40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
41
42 </inputs>
43
44 <outputs>
45 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
46
47 </outputs>
48
49 <help><![CDATA[
50 Fastq stats with vsearch.
51 ###############################################################
52
53 A fastq overview via vsearch's fastq_stats, fastq_eestats and
54 fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch
55 for detailed documentation of these tools.
56
57 Parameters
58 ----------
59 sequences : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
60 Fastq sequences
61 threads : Int % Range(1, None) | Str % Choices('auto'), optional
62 The number of threads used for computation.
63
64 Returns
65 -------
66 visualization : Visualization
67 ]]></help>
68 <macros>
69 <import>qiime_citation.xml</import>
70 </macros>
71 <expand macro="qiime_citation"/>
72 </tool>