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comparison qiime2/qiime_demux_summarize.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_summarize" name="qiime demux summarize" version="2019.4">
3 <description> - Summarize counts per sample.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime demux summarize
9
10 --i-data=$idata
11
12 #if $pn:
13 --p-n=$pn
14 #end if
15
16 --o-visualization=ovisualization
17 ;
18 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
19 && cp -r out/* '$ovisualization.files_path'
20 && mv '$ovisualization.files_path/index.html' '$ovisualization'
21 ]]></command>
22 <inputs>
23 <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be summarized. [required]" name="idata" optional="False" type="data"/>
24 <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"/>
25 </inputs>
26 <outputs>
27 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
28 </outputs>
29 <help><![CDATA[
30 Summarize counts per sample.
31 ############################
32
33 Summarize counts per sample for all samples, and generate interactive
34 positional quality plots based on `n` randomly selected sequences.
35
36 Parameters
37 ----------
38 data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
39 The demultiplexed sequences to be summarized.
40 n : Int, optional
41 The number of sequences that should be selected at random for quality
42 score plots. The quality plots will present the average positional
43 qualities across all of the sequences selected. If input sequences are
44 paired end, plots will be generated for both forward and reverse reads
45 for the same `n` sequences.
46
47 Returns
48 -------
49 visualization : Visualization
50 ]]></help>
51 <macros>
52 <import>qiime_citation.xml</import>
53 </macros>
54 <expand macro="qiime_citation"/>
55 </tool>