--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-control_evaluate-seqs.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,80 @@
+<?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>
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