--- a/qiime2/qiime_quality-control_exclude-seqs.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_quality-control_exclude-seqs.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,62 +1,74 @@
 <?xml version="1.0" ?>
-<tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2019.7">
-	<description> - Exclude sequences by alignment</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs"
+      version="2020.8">
+  <description>Exclude sequences by alignment</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime quality-control exclude-seqs
 
 --i-query-sequences=$iquerysequences
+
 --i-reference-sequences=$ireferencesequences
 
 #if str($pmethod) != 'None':
- --p-method=$pmethod
+--p-method=$pmethod
 #end if
 
-#if str($ppercidentity):
- --p-perc-identity=$ppercidentity
-#end if
+--p-perc-identity=$ppercidentity
 
 #if str($pevalue):
- --p-evalue="$pevalue"
+  --p-evalue=$pevalue
 #end if
+--p-perc-query-aligned=$ppercqueryaligned
 
-#if str($ppercqueryaligned):
- --p-perc-query-aligned=$ppercqueryaligned
-#end if
+--p-threads=$pthreads
 
-#set $pthreads = '${GALAXY_SLOTS:-4}'
-#if str($pthreads):
- --p-threads="$pthreads"
+#if str($pleftjustify) != 'None':
+--p-left-justify=$pleftjustify
 #end if
 
 --o-sequence-hits=osequencehits
+
 --o-sequence-misses=osequencemisses
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp osequencehits.qza $osequencehits;
 cp osequencemisses.qza $osequencemisses
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion              [required]" name="iquerysequences" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences [required]" name="ireferencesequences" optional="False" type="data"/>
-		<param label="--p-method: " name="pmethod" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="blast">blast</option>
-			<option value="vsearch">vsearch</option>
-			<option value="blastn-short">blastn-short</option>
-		</param>
-		<param label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]      [default: 0.97]" name="ppercidentity" optional="True" type="float" value="0.97" min="0" max="1" exclusive_end="False"/>
-		<param label="--p-evalue: NUMBER    BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.            [optional]" name="pevalue" optional="True" type="float"/>
-		<param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit.       [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits"/>
-		<data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></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="--p-method: " name="pmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="blast">blast</option>
+      <option value="blastn-short">blastn-short</option>
+    </param>
+    <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]   [default: 0.97]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.97" />
+    <param label="--p-evalue: NUMBER       BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.    [optional]" name="pevalue" optional="False" type="text" />
+    <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97" />
+    <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="False">False</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: sequencehits.qza" name="osequencehits" />
+    <data format="qza" label="${tool.name} on ${on_string}: sequencemisses.qza" name="osequencemisses" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Exclude sequences by alignment
-##############################
+###############################################################
 
 This method aligns feature sequences to a set of reference sequences to
 identify sequences that hit/miss the reference within a specified
@@ -76,7 +88,7 @@
     Sequences to test for exclusion
 reference_sequences : FeatureData[Sequence]
     Reference sequences to align against feature sequences
-method : Str % Choices('blast', 'vsearch', 'blastn-short'), optional
+method : Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')², optional
     Alignment method to use for matching feature sequences against
     reference sequences
 perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
@@ -88,6 +100,10 @@
 perc_query_aligned : Float, optional
     Percent of query sequence that must align to reference in order to be
     accepted as a hit.
+threads : Int % Range(1, None), optional
+    Number of jobs to execute. Only applies to vsearch method.
+left_justify : Bool % Choices(False)¹ | Bool², optional
+    Reject match if the pairwise alignment begins with gaps
 
 Returns
 -------
@@ -95,9 +111,9 @@
     Subset of feature sequences that align to reference sequences
 sequence_misses : FeatureData[Sequence]
     Subset of feature sequences that do not align to reference sequences
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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