view qiime2__gneiss__ilr_phylogenetic_differential.xml @ 1:f37156e185ea draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 69da7976573cc07a363ac66bdacc9269d7cd3732

<?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: 2022.11.1)
for:
    qiime2 (version: 2022.11.1)
-->
<tool name="qiime2 gneiss ilr-phylogenetic-differential" id="qiime2__gneiss__ilr_phylogenetic_differential" version="2022.11.1+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Differentially abundant Phylogenetic Log Ratios.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.11</container>
    </requirements>
    <version_command>q2galaxy version gneiss</version_command>
    <command detect_errors="exit_code">q2galaxy run gneiss ilr_phylogenetic_differential '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="differential" type="data" format="qza" label="differential: FeatureData[Differential]" help="[required]  The differential abundance results in which will be ilr transformed.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Differential]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Differential]']</validator>
        </param>
        <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required]  A rooted phylogeny of feature identifiers that defines the partitions of features.  Each tip in the hierarchycorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.  This assumes that all of the internal nodes in the tree have labels. This tree may contain polytomic nodes (i.e., nodes with more than two children), in which case they will be bifurcated.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="Phylogeny[Rooted]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator>
        </param>
    </inputs>
    <outputs>
        <data name="ilr_differential" format="qza" label="${tool.name} on ${on_string}: ilr_differential.qza" from_work_dir="ilr_differential.qza"/>
        <data name="bifurcated_tree" format="qza" label="${tool.name} on ${on_string}: bifurcated_tree.qza" from_work_dir="bifurcated_tree.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: gneiss ilr-phylogenetic-differential
=============================================
Differentially abundant Phylogenetic Log Ratios.


Outputs:
--------
:ilr_differential.qza: Per clade differential abundance results.
:bifurcated_tree.qza: Bifurcating phylogeny.

|  

Description:
------------
Compute an ILR transform of differentials given a rooted phylogeny.


|  

</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>