view qiime2/qiime_quality-filter_q-score.xml @ 8:d66c7509e8f9 draft

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<?xml version="1.0" ?>
<tool id="qiime_quality-filter_q-score" name="qiime quality-filter q-score" version="2019.4">
	<description> - Quality filter based on sequence quality scores.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime quality-filter q-score

--i-demux=$idemux

#if str($pminquality):
 --p-min-quality=$pminquality
#end if

#if str($pqualitywindow):
 --p-quality-window=$pqualitywindow
#end if

#if str($pminlengthfraction):
 --p-min-length-fraction=$pminlengthfraction
#end if

#if str($pmaxambiguous):
 --p-max-ambiguous=$pmaxambiguous
#end if

--o-filtered-sequences=ofilteredsequences
--o-filter-stats=ofilterstats
;
cp ofilteredsequences.qza $ofilteredsequences;
cp ofilterstats.qza $ofilterstats
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] The demultiplexed sequence data to be quality filtered.                                    [required]" name="idemux" optional="False" type="data"/>
		<param label="--p-min-quality: INTEGER The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores.                                    [default: 4]" name="pminquality" optional="True" type="integer" value="4"/>
		<param label="--p-quality-window: INTEGER The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read.                             [default: 3]" name="pqualitywindow" optional="True" type="integer" value="3"/>
		<param label="--p-min-length-fraction: NUMBER The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length.                                 [default: 0.75]" name="pminlengthfraction" optional="True" type="float" value="0.75"/>
		<param label="--p-max-ambiguous: INTEGER The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min-length-fraction`.                     [default: 0]" name="pmaxambiguous" optional="True" type="integer" value="0"/>
	</inputs>
	<outputs>
		<data format="qza" label="${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]
    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]
    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>