--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_quality-control_exclude-seqs.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,119 @@
+<?xml version="1.0" ?>
+<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
+#end if
+
+--p-perc-identity=$ppercidentity
+
+#if str($pevalue):
+  --p-evalue=$pevalue
+#end if
+--p-perc-query-aligned=$ppercqueryaligned
+
+--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 osequencemisses.qza $osequencemisses
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-query-sequences: ARTIFACT FeatureData[Sequence] Sequences to test for exclusion           [required]" name="iquerysequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] Reference sequences to align against feature sequences                                 [required]" name="ireferencesequences" optional="False" type="data" />
+    <param label="--p-method: " name="pmethod" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="blast">blast</option>
+      <option value="blastn-short">blastn-short</option>
+    </param>
+    <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]   [default: 0.97]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.97" />
+    <param label="--p-evalue: NUMBER       BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.    [optional]" name="pevalue" optional="False" type="text" />
+    <param label="--p-perc-query-aligned: NUMBER Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97" />
+    <param label="--p-left-justify: " name="pleftjustify" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="False">False</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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
+perc_identity, evalue, and perc_query_aligned. This method could be used to
+define a positive filter, e.g., extract only feature sequences that align
+to a certain clade of bacteria; or to define a negative filter, e.g.,
+identify sequences that align to contaminant or human DNA sequences that
+should be excluded from subsequent analyses. Note that filtering is
+performed based on the perc_identity, perc_query_aligned, and evalue
+thresholds (the latter only if method==BLAST and an evalue is set). Set
+perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
+thresholds as necessary.
+
+Parameters
+----------
+query_sequences : FeatureData[Sequence]
+    Sequences to test for exclusion
+reference_sequences : FeatureData[Sequence]
+    Reference sequences to align against feature sequences
+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
+    Reject match if percent identity to reference is lower. Must be in
+    range [0.0, 1.0]
+evalue : Float, optional
+    BLAST expectation (E) value threshold for saving hits. Reject if E
+    value is higher than threshold. This threshold is disabled by default.
+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
+-------
+sequence_hits : FeatureData[Sequence]
+    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>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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