<?xml version="1.0" ?>
<tool id="qiime_quality-control_evaluate-seqs" name="qiime quality-control evaluate-seqs" version="2018.4">
	<description> - Compare query (observed) vs. reference (expected) sequences.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime quality-control evaluate-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig

	#if $pshowalignments:
		--p-show-alignments
	#else
		--p-no-show-alignments
	#end if

	#end if
	 --o-visualization=ovisualization;

	qiime tools export ovisualization.qzv --output-dir 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: FeatureData[Sequence] Sequences to test for exclusion  [required]" name="iquerysequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] Reference sequences to align against feature sequences  [required]" name="ireferencesequences" optional="False" type="data"/>

		<param label="  --p-show-alignments / --p-no-show-alignments
                                  Option to plot pairwise alignments of query
                                  sequences and their top hits.  [default:
                                  False]" name="pshowalignments" checked="False" type="boolean"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" 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>