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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:33:04 +0000 |
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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>