annotate qiime2__gneiss__ilr_hierarchical.xml @ 2:d0feca181800 draft default tip

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 65e4952f33eb335528e8553150e9097e5ea8f556

<?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 gneiss ilr-hierarchical" id="qiime2__gneiss__ilr_hierarchical" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Isometric Log-ratio Transform applied to a hierarchical clustering</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2023.5</container>
    </requirements>
    <version_command>q2galaxy version gneiss</version_command>
    <command detect_errors="exit_code">q2galaxy run gneiss ilr_hierarchical '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | Composition]" help="[required]  The feature table containing the samples in which the ilr transform will be performed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureTable[Composition]"/>
                <filter type="add_value" value="FeatureTable[Frequency]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]']</validator>
        </param>
        <param name="tree" type="data" format="qza" label="tree: Hierarchy" help="[required]  A hierarchy of feature identifiers that defines the partitions of features.  Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.  This assumes that all of the internal nodes in the tree have labels.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Hierarchy"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Hierarchy']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <param name="pseudocount" type="float" value="0.5" label="pseudocount: Float" help="[default: 0.5]  The value to add to zero counts in the feature table."/>
        </section>
    </inputs>
    <outputs>
        <data name="balances" format="qza" label="${tool.name} on ${on_string}: balances.qza" from_work_dir="balances.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: gneiss ilr-hierarchical
================================
Isometric Log-ratio Transform applied to a hierarchical clustering


Outputs:
--------
:balances.qza: The resulting balances from the ilr transform.

|  

Description:
------------
Calculate balances given a hierarchy.


|  

</help>
    <citations>
        <citation type="bibtex">@article{cite1,
 author = {Morton, James T and Sanders, Jon and Quinn, Robert A and McDonald, Daniel and Gonzalez, Antonio and Vázquez-Baeza, Yoshiki and Navas-Molina, Jose A and Song, Se Jin and Metcalf, Jessica L and Hyde, Embriette R and Lladser, Manuel and Dorrestein, Pieter C and Knight, Rob},
 journal = {MSystems},
 number = {1},
 pages = {e00162--16},
 publisher = {Am Soc Microbiol},
 title = {Balance trees reveal microbial niche differentiation},
 volume = {2},
 year = {2017}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>