<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2024, QIIME 2 development team.

Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
-->
<!--
This tool was automatically generated by:
    q2galaxy (version: 2024.2.1)
for:
    qiime2 (version: 2024.2.0)
-->
<tool name="qiime2 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Quality filter based on sequence quality scores.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version quality_filter</version_command>
    <command detect_errors="exit_code">q2galaxy run quality_filter q_score '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²" help="[required]  The demultiplexed sequence data to be quality filtered.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]"/>
                <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="min_quality" type="integer" value="4" label="min_quality: Int" help="[default: 4]  The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores."/>
            <param name="quality_window" type="integer" value="3" label="quality_window: Int" help="[default: 3]  The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read."/>
            <param name="min_length_fraction" type="float" value="0.75" label="min_length_fraction: Float" help="[default: 0.75]  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."/>
            <param name="max_ambiguous" type="integer" value="0" label="max_ambiguous: Int" help="[default: 0]  The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min_length_fraction`."/>
        </section>
    </inputs>
    <outputs>
        <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/>
        <data name="filter_stats" format="qza" label="${tool.name} on ${on_string}: filter_stats.qza" from_work_dir="filter_stats.qza"/>
    </outputs>
    <tests>
        <test>
            <param name="demux" value="q_score.test0.demuxed-seqs.qza" ftype="qza"/>
            <output name="filtered_sequences" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/>
                    </has_archive_member>
                </assert_contents>
            </output>
            <output name="filter_stats" ftype="qza">
                <assert_contents>
                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
                        <has_line_matching expression="type: QualityFilterStats"/>
                    </has_archive_member>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
QIIME 2: quality-filter q-score
===============================
Quality filter based on sequence quality scores.


Outputs:
--------
:filtered_sequences.qza: The resulting quality-filtered sequences.
:filter_stats.qza: Summary statistics of the filtering process.

|  

Description:
------------
This method filters sequence based on quality scores and the presence of ambiguous base calls.

Examples:
---------

q_score
*******
Using the ``qiime2 quality-filter q-score`` tool:
 #. Set *"demux"* to ``#: demuxed-seqs.qza``
 #. Press the ``Execute`` button.

Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
 (Renaming is optional, but it will make any subsequent steps easier to complete.)

 .. list-table::
    :align: left
    :header-rows: 1

    * - History Name
      - *"Name"* to set (be sure to press ``Save``)
    * - ``#: qiime2 quality-filter q-score [...] : filtered_sequences.qza``
      - ``dumux-filtered.qza``
    * - ``#: qiime2 quality-filter q-score [...] : filter_stats.qza``
      - ``demux-filter-stats.qza``


|  

</help>
    <citations>
        <citation type="doi">10.1038/nmeth.2276</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>