Mercurial > repos > q2d2 > qiime2__gneiss__dendrogram_heatmap

view qiime2__gneiss__dendrogram_heatmap.xml @ 2:78bd3306c2d5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 65e4952f33eb335528e8553150e9097e5ea8f556
author q2d2
date Thu, 08 Jun 2023 19:48:23 +0000
parents ec24bc691af1
children
line wrap: on
line source

<?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 dendrogram-heatmap" id="qiime2__gneiss__dendrogram_heatmap" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
    <description>Dendrogram heatmap.</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 dendrogram_heatmap '$inputs'</command>
    <configfiles>
        <inputs name="inputs" data_style="paths"/>
    </configfiles>
    <inputs>
        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values.">
            <options options_filter_attribute="metadata.semantic_type">
                <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[Frequency]']</validator>
        </param>
        <param name="tree" type="data" format="qza" label="tree: Hierarchy" help="[required]  A hierarchy of feature identifiers where each tipcorresponds 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.">
            <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>
        <conditional name="metadata">
            <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required]  Categorical metadata column to group the samples.">
                <option value="tsv" selected="true">Metadata from TSV</option>
                <option value="qza">Metadata from Artifact</option>
            </param>
            <when value="tsv">
                <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
                <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
                    <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
                </param>
            </when>
            <when value="qza">
                <param name="source" type="data" format="qza" label="Metadata Source"/>
                <param name="column" type="text" label="Column Name">
                    <validator type="empty_field"/>
                </param>
            </when>
        </conditional>
        <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 pseudocount to add to avoid division by zero."/>
            <param name="ndim" type="integer" value="10" label="ndim: Int" help="[default: 10]  Number of dimensions to highlight."/>
            <param name="method" type="select" label="method: Str % Choices('clr', 'log')" display="radio">
                <option value="clr" selected="true">clr</option>
                <option value="log">log</option>
            </param>
            <param name="color_map" type="select" label="color_map: Str % Choices('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism')">
                <option value="viridis" selected="true">viridis</option>
                <option value="inferno">inferno</option>
                <option value="plasma">plasma</option>
                <option value="magma">magma</option>
                <option value="Blues">Blues</option>
                <option value="BuGn">BuGn</option>
                <option value="BuPu">BuPu</option>
                <option value="GnBu">GnBu</option>
                <option value="Greens">Greens</option>
                <option value="Greys">Greys</option>
                <option value="Oranges">Oranges</option>
                <option value="OrRd">OrRd</option>
                <option value="PuBu">PuBu</option>
                <option value="PuBuGn">PuBuGn</option>
                <option value="PuRd">PuRd</option>
                <option value="Purples">Purples</option>
                <option value="RdPu">RdPu</option>
                <option value="Reds">Reds</option>
                <option value="YlGn">YlGn</option>
                <option value="YlGnBu">YlGnBu</option>
                <option value="YlOrBr">YlOrBr</option>
                <option value="YlOrRd">YlOrRd</option>
                <option value="afmhot">afmhot</option>
                <option value="autumn">autumn</option>
                <option value="bone">bone</option>
                <option value="cool">cool</option>
                <option value="copper">copper</option>
                <option value="gist_heat">gist_heat</option>
                <option value="gray">gray</option>
                <option value="hot">hot</option>
                <option value="pink">pink</option>
                <option value="spring">spring</option>
                <option value="summer">summer</option>
                <option value="winter">winter</option>
                <option value="BrBG">BrBG</option>
                <option value="bwr">bwr</option>
                <option value="coolwarm">coolwarm</option>
                <option value="PiYG">PiYG</option>
                <option value="PRGn">PRGn</option>
                <option value="PuOr">PuOr</option>
                <option value="RdBu">RdBu</option>
                <option value="RdGy">RdGy</option>
                <option value="RdYlBu">RdYlBu</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="Spectral">Spectral</option>
                <option value="seismic">seismic</option>
                <option value="Accent">Accent</option>
                <option value="Dark2">Dark2</option>
                <option value="Paired">Paired</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel2">Pastel2</option>
                <option value="Set1">Set1</option>
                <option value="Set2">Set2</option>
                <option value="Set3">Set3</option>
                <option value="Vega10">Vega10</option>
                <option value="Vega20">Vega20</option>
                <option value="Vega20b">Vega20b</option>
                <option value="Vega20c">Vega20c</option>
                <option value="gist_earth">gist_earth</option>
                <option value="terrain">terrain</option>
                <option value="ocean">ocean</option>
                <option value="gist_stern">gist_stern</option>
                <option value="brg">brg</option>
                <option value="CMRmap">CMRmap</option>
                <option value="cubehelix">cubehelix</option>
                <option value="gnuplot">gnuplot</option>
                <option value="gnuplot2">gnuplot2</option>
                <option value="gist_ncar">gist_ncar</option>
                <option value="nipy_spectral">nipy_spectral</option>
                <option value="jet">jet</option>
                <option value="rainbow">rainbow</option>
                <option value="gist_rainbow">gist_rainbow</option>
                <option value="hsv">hsv</option>
                <option value="flag">flag</option>
                <option value="prism">prism</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: gneiss dendrogram-heatmap
==================================
Dendrogram heatmap.


Outputs:
--------
:visualization.qzv: &lt;no description&gt;

|  

Description:
------------
Visualize the feature table as a heatmap, with samples sorted along a specified categorical metadata column and features clustered together specified by the tree.


|  

</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>