--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_quality-filter_q-score.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,85 @@
+<?xml version="1.0" ?>
+<tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score"
+      version="2020.8">
+  <description>Quality filter based on sequence quality scores.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime quality-filter q-score
+
+--i-demux=$idemux
+
+--p-min-quality=$pminquality
+
+--p-quality-window=$pqualitywindow
+
+--p-min-length-fraction=$pminlengthfraction
+
+--p-max-ambiguous=$pmaxambiguous
+
+--o-filtered-sequences=ofilteredsequences
+
+--o-filter-stats=ofilterstats
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ofilterstats.qza $ofilterstats
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]² The demultiplexed sequence data to be quality filtered.                                    [required]" name="idemux" optional="False" type="data" />
+    <param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores.                                    [default: 4]" name="pminquality" optional="True" type="integer" value="4" />
+    <param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read.                             [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3" />
+    <param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length.                                 [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75" />
+    <param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`.                     [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: filteredsequences.qza" name="ofilteredsequences" />
+    <data format="qza" label="${tool.name} on ${on_string}: filterstats.qza" name="ofilterstats" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Quality filter based on sequence quality scores.
+###############################################################
+
+This method filters sequence based on quality scores and the presence of
+ambiguous base calls.
+
+Parameters
+----------
+demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
+    The demultiplexed sequence data to be quality filtered.
+min_quality : Int, optional
+    The minimum acceptable PHRED score. All PHRED scores less that this
+    value are considered to be low PHRED scores.
+quality_window : Int, optional
+    The maximum number of low PHRED scores that can be observed in direct
+    succession before truncating a sequence read.
+min_length_fraction : Float, optional
+    The minimum length that a sequence read can be following truncation and
+    still be retained. This length should be provided as a fraction of the
+    input sequence length.
+max_ambiguous : Int, optional
+    The maximum number of ambiguous (i.e., N) base calls. This is applied
+    after trimming sequences based on `min_length_fraction`.
+
+Returns
+-------
+filtered_sequences : SampleData[SequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
+    The resulting quality-filtered sequences.
+filter_stats : QualityFilterStats
+    Summary statistics of the filtering process.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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