comparison qiime2__fragment_insertion__sepp.xml @ 3:f900d65ea217 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

2:2fa85eae206e

<?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: 2023.5.0)
for:
    qiime2 (version: 2023.5.1)
-->
<tool name="qiime2 fragment-insertion sepp" id="qiime2__fragment_insertion__sepp" version="2023.5.0+q2galaxy.2023.5.0.2" 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:2023.5</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]"/>

            <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"/>

3:f900d65ea217

<?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 fragment-insertion sepp" id="qiime2__fragment_insertion__sepp" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Insert fragment sequences using SEPP into reference phylogenies.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</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="staging_path_and_source_path"/>
    </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]"/>

            <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="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"/>