<?xml version="1.0" ?>
<tool id="qiime_quality-control_bowtie2-build" name="qiime quality-control bowtie2-build"
      version="2020.8">
  <description>Build bowtie2 index from reference sequences.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime quality-control bowtie2-build

--i-sequences=$isequences

--p-n-threads=$pnthreads

--o-database=odatabase

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

;
cp odatabase.qza $odatabase

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] Reference sequences used to build bowtie2 index. [required]" name="isequences" optional="False" type="data" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: database.qza" name="odatabase" />
    
  </outputs>

  <help><![CDATA[
Build bowtie2 index from reference sequences.
###############################################################

Build bowtie2 index from reference sequences.

Parameters
----------
sequences : FeatureData[Sequence]
    Reference sequences used to build bowtie2 index.
n_threads : Int % Range(1, None), optional
    Number of threads to launch

Returns
-------
database : Bowtie2Index
    Bowtie2 index.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>