<?xml version="1.0" ?>
<tool id="qiime_demux_summarize" name="qiime demux summarize" version="2019.4">
	<description> - Summarize counts per sample.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime demux summarize

--i-data=$idata

#if str($pn):
 --p-n=$pn
#end if

--o-visualization=ovisualization
;
qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'
	]]></command>
	<inputs>
		<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"/>
		<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"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Summarize counts per sample.
############################

Summarize counts per sample for all samples, and generate interactive
positional quality plots based on `n` randomly selected sequences.

Parameters
----------
data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
    The demultiplexed sequences to be summarized.
n : Int, optional
    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.

Returns
-------
visualization : Visualization
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>