comparison qiime2__phylogeny__iqtree.xml @ 2:2f898b3531ee draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 65e4952f33eb335528e8553150e9097e5ea8f556

1:931254bf17a4

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 phylogeny iqtree" id="qiime2__phylogeny__iqtree" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Construct a phylogenetic tree with IQ-TREE.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="exit_code">q2galaxy run phylogeny iqtree '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>

            <param name="stop_iter" type="integer" min="1" optional="true" label="stop_iter: Int % Range(1, None)" help="[optional]  Number of unsuccessful iterations to stop. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="perturb_nni_strength" type="float" min="0.01" max="0.999999" optional="true" label="perturb_nni_strength: Float % Range(0.01, 1.0)" help="[optional]  Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="spr_radius" type="integer" min="1" optional="true" label="spr_radius: Int % Range(1, None)" help="[optional]  Radius for parsimony SPR search. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No]  Perform more thorough NNI search."/>
            <param name="fast" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="fast: Bool" help="[default: No]  Fast search to resemble FastTree."/>
            <param name="alrt" type="integer" min="1000" optional="true" label="alrt: Int % Range(1000, None)" help="[optional]  Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="abayes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="abayes: Bool" help="[default: No]  Single branch test method. Approximate Bayes test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="lbp" type="integer" min="1000" optional="true" label="lbp: Int % Range(1000, None)" help="[optional]  Single branch test method. Number of bootstrap replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is recomended. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="safe" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="safe: Bool" help="[default: No]  Safe likelihood kernel to avoid numerical underflow."/>
        </section>
    </inputs>
    <outputs>
        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>

2:2f898b3531ee

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 iqtree" id="qiime2__phylogeny__iqtree" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Construct a phylogenetic tree with IQ-TREE.</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 iqtree '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>

            <param name="stop_iter" type="integer" min="1" optional="true" label="stop_iter: Int % Range(1, None)" help="[optional]  Number of unsuccessful iterations to stop. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="perturb_nni_strength" type="float" min="0.01" max="0.999999" optional="true" label="perturb_nni_strength: Float % Range(0.01, 1.0)" help="[optional]  Perturbation strength for randomized NNI. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="spr_radius" type="integer" min="1" optional="true" label="spr_radius: Int % Range(1, None)" help="[optional]  Radius for parsimony SPR search. If not set, program defaults will be used. See IQ-TREE manual for details."/>
            <param name="allnni" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allnni: Bool" help="[default: No]  Perform more thorough NNI search."/>
            <param name="fast" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="fast: Bool" help="[default: No]  Fast search to resemble FastTree."/>
            <param name="alrt" type="integer" min="1000" optional="true" label="alrt: Int % Range(1000, None)" help="[optional]  Single branch test method. Number of bootstrap replicates to perform an SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000 replicates is required. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="abayes" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="abayes: Bool" help="[default: No]  Single branch test method. Approximate Bayes test. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="lbp" type="integer" min="1000" optional="true" label="lbp: Int % Range(1000, None)" help="[optional]  Single branch test method. Number of bootstrap replicates to perform a fast local bootstrap probability method. Minimum of 1000 replicates is required. Can be used with other 'single branch test methods'. Values reported in the order of: alrt, lbp, abayes."/>
            <param name="safe" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="safe: Bool" help="[default: No]  Safe likelihood kernel to avoid numerical underflow."/>
        </section>
    </inputs>
    <outputs>
        <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/>