<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2023, 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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 fragment-insertion sepp" id="qiime2__fragment_insertion__sepp" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version fragment_insertion</version_command>
    <command detect_errors="exit_code">q2galaxy run fragment_insertion sepp '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="representative_sequences" type="data" format="qza" label="representative_sequences: FeatureData[Sequence]" help="[required]  The sequences to insert into the reference tree.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Sequence]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
        </param>
        <param name="reference_database" type="data" format="qza" label="reference_database: SeppReferenceDatabase" help="[required]  The reference database to insert the representative sequences into.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="SeppReferenceDatabase"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SeppReferenceDatabase']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="alignment_subset_size" type="integer" value="1000" label="alignment_subset_size: Int" help="[default: 1000]  Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset."/>
            <param name="placement_subset_size" type="integer" value="5000" label="placement_subset_size: Int" help="[default: 5000]  The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/sepp-tutorial.md#sample-datasets-default-parameters."/>
            <param name="threads" type="integer" value="1" label="threads: Int" help="[default: 1]  The number of threads to use."/>
            <param name="debug" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="debug: Bool" help="[default: No]  Collect additional run information to STDOUT for debugging. Temporary directories will not be removed if run fails."/>
        </section>
    </inputs>
    <outputs>
        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>
        <data name="placements" format="qza" label="${tool.name} on ${on_string}: placements.qza" from_work_dir="placements.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: fragment-insertion sepp
================================
Insert fragment sequences using SEPP into reference phylogenies.


Outputs:
--------
:tree.qza: The tree with inserted feature data.
:placements.qza: Information about the feature placements within the reference tree.

|  

Description:
------------
Perform fragment insertion of sequences using the SEPP algorithm.


|  

</help>
    <citations>
        <citation type="doi">10.1128/mSystems.00021-18</citation>
        <citation type="doi">10.1371/journal.pone.0031009</citation>
        <citation type="doi">10.1371/journal.pcbi.1002195</citation>
        <citation type="bibtex">@article{cite4,
 author = {Matsen, Frederick A and Kodner, Robin B and Armbrust, E Virginia},
 journal = {BMC bioinformatics},
 number = {1},
 pages = {538},
 publisher = {BioMed Central},
 title = {pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree},
 volume = {11},
 year = {2010}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>