annotate qiime2__rescript__degap_seqs.xml @ 2:cbbe64c579b2 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7

<?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: 2024.10.0)
for:
    qiime2 (version: 2024.10.1)
-->
<tool name="qiime2 rescript degap-seqs" id="qiime2__rescript__degap_seqs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
    <description>Remove gaps from DNA sequence alignments.</description>
    <xrefs>
        <xref type="bio.tools">qiime2</xref>
    </xrefs>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
    </requirements>
    <version_command>q2galaxy version rescript</version_command>
    <command detect_errors="exit_code">q2galaxy run rescript degap_seqs '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="aligned_sequences" type="data" format="qza" label="aligned_sequences: FeatureData[AlignedSequence]" help="[required]  Aligned DNA Sequences to be degapped.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="min_length" type="integer" min="1" value="1" label="min_length: Int % Range(1, None)" help="[default: 1]  Minimum length of sequence to be returned after degapping."/>
        </section>
    </inputs>
    <outputs>
        <data name="degapped_sequences" format="qza" label="${tool.name} on ${on_string}: degapped_sequences.qza" from_work_dir="degapped_sequences.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: rescript degap-seqs
============================
Remove gaps from DNA sequence alignments.


Outputs:
--------
:degapped_sequences.qza: The resulting unaligned (degapped) DNA sequences.

|  

Description:
------------
This method converts aligned DNA sequences to unaligned DNA sequences by removing gaps ("-") and missing data (".") characters from the sequences. Essentially, 'unaligning' the sequences.


|  

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