comparison qiime2__phylogeny__raxml.xml @ 3:a516b3efde8d draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

2:2ff23f0ed1ba

<?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 phylogeny raxml" id="qiime2__phylogeny__raxml" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Construct a phylogenetic tree with RAxML.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="exit_code">q2galaxy run phylogeny raxml '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  Aligned sequences to be used for phylogenetic reconstruction.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>

            <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="seed" type="integer" optional="true" label="seed: Int" help="[optional]  Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
            <param name="n_searches" type="integer" min="1" value="1" label="n_searches: Int % Range(1, None)" help="[default: 1]  The number of independent maximum likelihood searches to perform. The single best scoring tree is returned."/>
            <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML."/>
            <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
                <option value="Standard" selected="true">Standard</option>
                <option value="SSE3">SSE3</option>
                <option value="AVX2">AVX2</option>
            </param>

3:a516b3efde8d

<?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 phylogeny raxml" id="qiime2__phylogeny__raxml" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
    <description>Construct a phylogenetic tree with RAxML.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="exit_code">q2galaxy run phylogeny raxml '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="staging_path_and_source_path"/>
    </configfiles>
    <inputs>
        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  Aligned sequences to be used for phylogenetic reconstruction.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[AlignedSequence]"/>

            <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="seed" type="integer" optional="true" label="seed: Int" help="[optional]  Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/>
            <param name="n_searches" type="integer" min="1" value="1" label="n_searches: Int % Range(1, None)" help="[default: 1]  The number of independent maximum likelihood searches to perform. The single best scoring tree is returned."/>
            <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio">
                <option value="Standard" selected="true">Standard</option>
                <option value="SSE3">SSE3</option>
                <option value="AVX2">AVX2</option>
            </param>