annotate qiime2__sample_classifier__heatmap.xml @ 0:9d749a1b0f69 draft

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 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 sample-classifier heatmap" id="qiime2__sample_classifier__heatmap" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
    <description>Generate heatmap of important features.</description>
    <requirements>
        <container type="docker">quay.io/qiime2/core:2022.8</container>
    </requirements>
    <version_command>q2galaxy version sample_classifier</version_command>
    <command detect_errors="aggressive">q2galaxy run sample_classifier 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]  Feature table containing all features that should be used for target prediction.">
            <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="importance" type="data" format="qza" label="importance: FeatureData[Importance]" help="[required]  Feature importances.">
            <options options_filter_attribute="metadata.semantic_type">
                <filter type="add_value" value="FeatureData[Importance]"/>
            </options>
            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Importance]']</validator>
        </param>
        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
            <conditional name="sample_metadata">
                <param name="type" type="select" label="sample_metadata: MetadataColumn[Categorical]" help="[optional]  Sample metadata column to use for sample labeling or grouping.">
                    <option value="none" selected="true">None (default)</option>
                    <option value="tsv">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="none"/>
                <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>
            <conditional name="feature_metadata">
                <param name="type" type="select" label="feature_metadata: MetadataColumn[Categorical]" help="[optional]  Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap.">
                    <option value="none" selected="true">None (default)</option>
                    <option value="tsv">Metadata from TSV</option>
                    <option value="qza">Metadata from Artifact</option>
                </param>
                <when value="none"/>
                <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>
            <param name="feature_count" type="integer" min="0" value="50" label="feature_count: Int % Range(0, None)" help="[default: 50]  Filter feature table to include top N most important features. Set to zero to include all features."/>
            <param name="importance_threshold" type="float" min="0" value="0" label="importance_threshold: Float % Range(0, None)" help="[default: 0]  Filter feature table to exclude any features with an importance score less than this threshold. Set to zero to include all features."/>
            <param name="group_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="group_samples: Bool" help="[default: No]  Group samples by sample metadata."/>
            <param name="normalize" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="normalize: Bool" help="[default: Yes]  Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table."/>
            <param name="missing_samples" type="select" label="missing_samples: Str % Choices('error', 'ignore')" display="radio">
                <option value="error">error</option>
                <option value="ignore" selected="true">ignore</option>
            </param>
            <param name="metric" type="select" label="metric: Str % Choices('braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
                <option value="braycurtis" selected="true">braycurtis</option>
                <option value="canberra">canberra</option>
                <option value="chebyshev">chebyshev</option>
                <option value="cityblock">cityblock</option>
                <option value="correlation">correlation</option>
                <option value="cosine">cosine</option>
                <option value="dice">dice</option>
                <option value="euclidean">euclidean</option>
                <option value="hamming">hamming</option>
                <option value="jaccard">jaccard</option>
                <option value="kulsinski">kulsinski</option>
                <option value="mahalanobis">mahalanobis</option>
                <option value="matching">matching</option>
                <option value="minkowski">minkowski</option>
                <option value="rogerstanimoto">rogerstanimoto</option>
                <option value="russellrao">russellrao</option>
                <option value="seuclidean">seuclidean</option>
                <option value="sokalmichener">sokalmichener</option>
                <option value="sokalsneath">sokalsneath</option>
                <option value="sqeuclidean">sqeuclidean</option>
                <option value="yule">yule</option>
            </param>
            <param name="method" type="select" label="method: Str % Choices('average', 'centroid', 'complete', 'median', 'single', 'ward', 'weighted')">
                <option value="average" selected="true">average</option>
                <option value="centroid">centroid</option>
                <option value="complete">complete</option>
                <option value="median">median</option>
                <option value="single">single</option>
                <option value="ward">ward</option>
                <option value="weighted">weighted</option>
            </param>
            <param name="cluster" type="select" label="cluster: Str % Choices('both', 'features', 'none', 'samples')" display="radio">
                <option value="both">both</option>
                <option value="features" selected="true">features</option>
                <option value="none">none</option>
                <option value="samples">samples</option>
            </param>
            <param name="color_scheme" type="select" label="color_scheme: Str % Choices('Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Vega10', 'Vega10_r', 'Vega20', 'Vega20_r', 'Vega20b', 'Vega20b_r', 'Vega20c', 'Vega20c_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cividis', 'cividis_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'icefire', 'icefire_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'mako', 'mako_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'rocket', 'rocket_r', 'seismic', 'seismic_r', 'spectral', 'spectral_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'viridis', 'viridis_r', 'vlag', 'vlag_r', 'winter', 'winter_r')">
                <option value="Accent">Accent</option>
                <option value="Accent_r">Accent_r</option>
                <option value="Blues">Blues</option>
                <option value="Blues_r">Blues_r</option>
                <option value="BrBG">BrBG</option>
                <option value="BrBG_r">BrBG_r</option>
                <option value="BuGn">BuGn</option>
                <option value="BuGn_r">BuGn_r</option>
                <option value="BuPu">BuPu</option>
                <option value="BuPu_r">BuPu_r</option>
                <option value="CMRmap">CMRmap</option>
                <option value="CMRmap_r">CMRmap_r</option>
                <option value="Dark2">Dark2</option>
                <option value="Dark2_r">Dark2_r</option>
                <option value="GnBu">GnBu</option>
                <option value="GnBu_r">GnBu_r</option>
                <option value="Greens">Greens</option>
                <option value="Greens_r">Greens_r</option>
                <option value="Greys">Greys</option>
                <option value="Greys_r">Greys_r</option>
                <option value="OrRd">OrRd</option>
                <option value="OrRd_r">OrRd_r</option>
                <option value="Oranges">Oranges</option>
                <option value="Oranges_r">Oranges_r</option>
                <option value="PRGn">PRGn</option>
                <option value="PRGn_r">PRGn_r</option>
                <option value="Paired">Paired</option>
                <option value="Paired_r">Paired_r</option>
                <option value="Pastel1">Pastel1</option>
                <option value="Pastel1_r">Pastel1_r</option>
                <option value="Pastel2">Pastel2</option>
                <option value="Pastel2_r">Pastel2_r</option>
                <option value="PiYG">PiYG</option>
                <option value="PiYG_r">PiYG_r</option>
                <option value="PuBu">PuBu</option>
                <option value="PuBuGn">PuBuGn</option>
                <option value="PuBuGn_r">PuBuGn_r</option>
                <option value="PuBu_r">PuBu_r</option>
                <option value="PuOr">PuOr</option>
                <option value="PuOr_r">PuOr_r</option>
                <option value="PuRd">PuRd</option>
                <option value="PuRd_r">PuRd_r</option>
                <option value="Purples">Purples</option>
                <option value="Purples_r">Purples_r</option>
                <option value="RdBu">RdBu</option>
                <option value="RdBu_r">RdBu_r</option>
                <option value="RdGy">RdGy</option>
                <option value="RdGy_r">RdGy_r</option>
                <option value="RdPu">RdPu</option>
                <option value="RdPu_r">RdPu_r</option>
                <option value="RdYlBu">RdYlBu</option>
                <option value="RdYlBu_r">RdYlBu_r</option>
                <option value="RdYlGn">RdYlGn</option>
                <option value="RdYlGn_r">RdYlGn_r</option>
                <option value="Reds">Reds</option>
                <option value="Reds_r">Reds_r</option>
                <option value="Set1">Set1</option>
                <option value="Set1_r">Set1_r</option>
                <option value="Set2">Set2</option>
                <option value="Set2_r">Set2_r</option>
                <option value="Set3">Set3</option>
                <option value="Set3_r">Set3_r</option>
                <option value="Spectral">Spectral</option>
                <option value="Spectral_r">Spectral_r</option>
                <option value="Vega10">Vega10</option>
                <option value="Vega10_r">Vega10_r</option>
                <option value="Vega20">Vega20</option>
                <option value="Vega20_r">Vega20_r</option>
                <option value="Vega20b">Vega20b</option>
                <option value="Vega20b_r">Vega20b_r</option>
                <option value="Vega20c">Vega20c</option>
                <option value="Vega20c_r">Vega20c_r</option>
                <option value="Wistia">Wistia</option>
                <option value="Wistia_r">Wistia_r</option>
                <option value="YlGn">YlGn</option>
                <option value="YlGnBu">YlGnBu</option>
                <option value="YlGnBu_r">YlGnBu_r</option>
                <option value="YlGn_r">YlGn_r</option>
                <option value="YlOrBr">YlOrBr</option>
                <option value="YlOrBr_r">YlOrBr_r</option>
                <option value="YlOrRd">YlOrRd</option>
                <option value="YlOrRd_r">YlOrRd_r</option>
                <option value="afmhot">afmhot</option>
                <option value="afmhot_r">afmhot_r</option>
                <option value="autumn">autumn</option>
                <option value="autumn_r">autumn_r</option>
                <option value="binary">binary</option>
                <option value="binary_r">binary_r</option>
                <option value="bone">bone</option>
                <option value="bone_r">bone_r</option>
                <option value="brg">brg</option>
                <option value="brg_r">brg_r</option>
                <option value="bwr">bwr</option>
                <option value="bwr_r">bwr_r</option>
                <option value="cividis">cividis</option>
                <option value="cividis_r">cividis_r</option>
                <option value="cool">cool</option>
                <option value="cool_r">cool_r</option>
                <option value="coolwarm">coolwarm</option>
                <option value="coolwarm_r">coolwarm_r</option>
                <option value="copper">copper</option>
                <option value="copper_r">copper_r</option>
                <option value="cubehelix">cubehelix</option>
                <option value="cubehelix_r">cubehelix_r</option>
                <option value="flag">flag</option>
                <option value="flag_r">flag_r</option>
                <option value="gist_earth">gist_earth</option>
                <option value="gist_earth_r">gist_earth_r</option>
                <option value="gist_gray">gist_gray</option>
                <option value="gist_gray_r">gist_gray_r</option>
                <option value="gist_heat">gist_heat</option>
                <option value="gist_heat_r">gist_heat_r</option>
                <option value="gist_ncar">gist_ncar</option>
                <option value="gist_ncar_r">gist_ncar_r</option>
                <option value="gist_rainbow">gist_rainbow</option>
                <option value="gist_rainbow_r">gist_rainbow_r</option>
                <option value="gist_stern">gist_stern</option>
                <option value="gist_stern_r">gist_stern_r</option>
                <option value="gist_yarg">gist_yarg</option>
                <option value="gist_yarg_r">gist_yarg_r</option>
                <option value="gnuplot">gnuplot</option>
                <option value="gnuplot2">gnuplot2</option>
                <option value="gnuplot2_r">gnuplot2_r</option>
                <option value="gnuplot_r">gnuplot_r</option>
                <option value="gray">gray</option>
                <option value="gray_r">gray_r</option>
                <option value="hot">hot</option>
                <option value="hot_r">hot_r</option>
                <option value="hsv">hsv</option>
                <option value="hsv_r">hsv_r</option>
                <option value="icefire">icefire</option>
                <option value="icefire_r">icefire_r</option>
                <option value="inferno">inferno</option>
                <option value="inferno_r">inferno_r</option>
                <option value="jet">jet</option>
                <option value="jet_r">jet_r</option>
                <option value="magma">magma</option>
                <option value="magma_r">magma_r</option>
                <option value="mako">mako</option>
                <option value="mako_r">mako_r</option>
                <option value="nipy_spectral">nipy_spectral</option>
                <option value="nipy_spectral_r">nipy_spectral_r</option>
                <option value="ocean">ocean</option>
                <option value="ocean_r">ocean_r</option>
                <option value="pink">pink</option>
                <option value="pink_r">pink_r</option>
                <option value="plasma">plasma</option>
                <option value="plasma_r">plasma_r</option>
                <option value="prism">prism</option>
                <option value="prism_r">prism_r</option>
                <option value="rainbow">rainbow</option>
                <option value="rainbow_r">rainbow_r</option>
                <option value="rocket" selected="true">rocket</option>
                <option value="rocket_r">rocket_r</option>
                <option value="seismic">seismic</option>
                <option value="seismic_r">seismic_r</option>
                <option value="spectral">spectral</option>
                <option value="spectral_r">spectral_r</option>
                <option value="spring">spring</option>
                <option value="spring_r">spring_r</option>
                <option value="summer">summer</option>
                <option value="summer_r">summer_r</option>
                <option value="tab10">tab10</option>
                <option value="tab10_r">tab10_r</option>
                <option value="tab20">tab20</option>
                <option value="tab20_r">tab20_r</option>
                <option value="tab20b">tab20b</option>
                <option value="tab20b_r">tab20b_r</option>
                <option value="tab20c">tab20c</option>
                <option value="tab20c_r">tab20c_r</option>
                <option value="terrain">terrain</option>
                <option value="terrain_r">terrain_r</option>
                <option value="viridis">viridis</option>
                <option value="viridis_r">viridis_r</option>
                <option value="vlag">vlag</option>
                <option value="vlag_r">vlag_r</option>
                <option value="winter">winter</option>
                <option value="winter_r">winter_r</option>
            </param>
        </section>
    </inputs>
    <outputs>
        <data name="heatmap" format="qzv" label="${tool.name} on ${on_string}: heatmap.qzv" from_work_dir="heatmap.qzv"/>
        <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/>
    </outputs>
    <tests/>
    <help>
QIIME 2: sample-classifier heatmap
==================================
Generate heatmap of important features.


Outputs:
--------
:heatmap.qzv: Heatmap of important features.
:filtered_table.qza: Filtered feature table containing data displayed in heatmap.

|  

Description:
------------
Generate a heatmap of important features. Features are filtered based on importance scores; samples are optionally grouped by sample metadata; and a heatmap is generated that displays (normalized) feature abundances per sample.


|  

</help>
    <citations>
        <citation type="doi">10.21105/joss.00934</citation>
        <citation type="bibtex">@article{cite2,
 author = {Pedregosa, Fabian and Varoquaux, Gaël and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard},
 journal = {Journal of machine learning research},
 number = {Oct},
 pages = {2825--2830},
 title = {Scikit-learn: Machine learning in Python},
 volume = {12},
 year = {2011}
}
</citation>
        <citation type="doi">10.1038/s41587-019-0209-9</citation>
    </citations>
</tool>