--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-control_evaluate-seqs.xml	Thu May 24 05:21:07 2018 -0400
@@ -0,0 +1,76 @@
+<?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>