<?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>