--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_fastq-stats.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -0,0 +1,72 @@
+<?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>
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