<?xml version="1.0" ?>
<tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs"
      version="2020.8">
  <description>Compare query (observed) vs. reference (expected) sequences.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime quality-control evaluate-seqs

--i-query-sequences=$iquerysequences

--i-reference-sequences=$ireferencesequences

--o-visualization=ovisualization

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

;
cp odatabase.qza $odatabase

;
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'

;
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-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion              [required]" name="iquerysequences" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data" />
    <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[
Compare query (observed) vs. reference (expected) sequences.
###############################################################

This action aligns a set of query (e.g., observed) sequences against a set
of reference (e.g., expected) sequences to evaluate the quality of
alignment. The intended use is to align observed sequences against expected
sequences (e.g., from a mock community) to determine the frequency of
mismatches between observed sequences and the most similar expected
sequences, e.g., as a measure of sequencing/method error. However, any
sequences may be provided as input to generate a report on pairwise
alignment quality against a set of reference sequences.

Parameters
----------
query_sequences : FeatureData[Sequence]
    Sequences to test for exclusion
reference_sequences : FeatureData[Sequence]
    Reference sequences to align against feature sequences
show_alignments : Bool, optional
    Option to plot pairwise alignments of query sequences and their top
    hits.

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