<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2025, 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: 2025.4.0)
for:
    qiime2 (version: 2025.4.0)
-->
<tool name="qiime2 rescript trim-alignment" id="qiime2__rescript__trim_alignment" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
    <description>Trim alignment based on provided primers or specific positions.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript trim_alignment '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="aligned_sequences" type="data" format="qza" label="aligned_sequences: FeatureData[AlignedSequence]" help="[required]  Aligned DNA sequences.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="__q2galaxy__GUI__conditional__primer_fwd__" label="primer_fwd: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="primer_fwd: Str" help="[optional]  Forward primer used to find the start position for alignment trimming. Provide as 5'-3'.">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="primer_fwd" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="primer_fwd" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <conditional name="__q2galaxy__GUI__conditional__primer_rev__" label="primer_rev: Str">
                <param name="__q2galaxy__GUI__select__" type="select" label="primer_rev: Str" help="[optional]  Reverse primer used to find the end position for alignment trimming. Provide as 5'-3'.">
                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
                    <option value="__q2galaxy__::control::provide">Provide a value</option>
                </param>
                <when value="__q2galaxy__::control::default">
                    <param name="primer_rev" type="hidden" value="__q2galaxy__::literal::None"/>
                </when>
                <when value="__q2galaxy__::control::provide">
                    <param name="primer_rev" type="text">
                        <sanitizer>
                            <valid initial="string.printable"/>
                        </sanitizer>
                    </param>
                </when>
            </conditional>
            <param name="position_start" type="integer" min="1" optional="true" label="position_start: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will begin. If not provided, alignment will not be trimmed at the beginning. If forward primer isspecified this parameter will be ignored."/>
            <param name="position_end" type="integer" min="1" optional="true" label="position_end: Int % Range(1, None)" help="[optional]  Position within the alignment where the trimming will end. If not provided, alignment will not be trimmed at the end. If reverse primer is specified this parameter will be ignored."/>
            <param name="keep_primer_location" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keep_primer_location: Bool" help="[default: No]  Retain the alignment positions of the primer binding location. Note: the primers themselves will be removed, but the alignment positions where the primers align will be retained in the alignment."/>
            <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  Number of threads to use for primer-based trimming, otherwise ignored. (Use `auto` to automatically use all available cores)"/>
        </section>
    </inputs>
    <outputs>
        <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript trim-alignment
================================
Trim alignment based on provided primers or specific positions.


Outputs:
--------
:trimmed_sequences.qza: Trimmed sequence alignment.

|  

Description:
------------
Trim an existing alignment based on provided primers or specific, pre-defined positions. Primers take precedence over the positions,i.e. if both are provided, positions will be ignored.When using primers in combination with a DNA alignment, a new alignment will be generated to locate primer positions. Subsequently, start (5'-most) and end (3'-most) position from fwd and rev primer located within the new alignment is identified and used for slicing the original alignment. The retention of alignment positions that span the primer locations can be toggled. WARNING: finding alignment positions via primer search can be inefficient for very large alignments and is only recommended for small alignments. For large alignments providing specific alignment positions is ideal.


|  

</help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1009581</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>