view qiime2-2020.8/qiime_vsearch_fastq-stats.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_vsearch_fastq-stats" name="qiime vsearch fastq-stats"
      version="2020.8">
  <description>Fastq stats with vsearch.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime vsearch fastq-stats

--i-sequences=$isequences

#if str($pthreads) != 'None':
--p-threads=$pthreads
#end if

--o-visualization=ovisualization

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp odereplicatedsequences.qza $odereplicatedsequences

;
qiime tools export  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-sequences: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] Fastq sequences                           [required]" name="isequences" optional="False" type="data" />
    <param label="--p-threads: " name="pthreads" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Int % Range(1">Int % Range(1</option>
      <option value="None">None</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
    
  </outputs>

  <help><![CDATA[
Fastq stats with vsearch.
###############################################################

A fastq overview via vsearch's fastq_stats, fastq_eestats and
fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch
for detailed documentation of these tools.

Parameters
----------
sequences : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]
    Fastq sequences
threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads used for computation.

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