annotate qiime2__phylogeny__robinson_foulds.xml @ 0:c27ffaac5054 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

<?xml version='1.0' encoding='utf-8'?>
<!--
Copyright (c) 2022, 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: 2022.8.1)
for:
    qiime2 (version: 2022.8.1)
-->
<tool name="qiime2 phylogeny robinson-foulds" id="qiime2__phylogeny__robinson_foulds" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version phylogeny</version_command>
    <command detect_errors="aggressive">q2galaxy run phylogeny robinson_foulds '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="trees" type="data" format="qza" label="trees: List[Phylogeny[Rooted | Unrooted]]" help="[required]  Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric." multiple="true">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Unrooted]"/>
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <repeat name="labels" help="[optional]  Labels to use for the tree names in the distance matrix. If ommited, labels will be &quot;tree_n&quot; where &quot;n&quot; ranges from 1..N. The number of labels must match the number of trees." title="labels: List[Str]">
                <param name="element" type="text" label="element: Str" help="[required]">
                    <sanitizer>
                        <valid initial="string.printable"/>
                    </sanitizer>
                    <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
                </param>
            </repeat>
            <param name="missing_tips" type="select" label="missing_tips: Str % Choices('error', 'intersect-all')" display="radio">
                <option value="error" selected="true">error</option>
                <option value="intersect-all">intersect-all</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: phylogeny robinson-foulds
==================================
Calculate Robinson-Foulds distance between phylogenetic trees.


Outputs:
--------
:distance_matrix.qza: The distances between trees as a symmetric matrix.

|  

Description:
------------
Calculate the Robinson-Foulds symmetric difference metric between two or more phylogenetic trees.


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Robinson, David F and Foulds, Leslie R},
 journal = {Mathematical biosciences},
 number = {1-2},
 pages = {131--147},
 publisher = {Elsevier},
 title = {Comparison of phylogenetic trees},
 volume = {53},
 year = {1981}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>