Mercurial > repos > q2d2 > qiime2__feature_table__heatmap
changeset 0:b4df421d7e75 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 19:56:45 +0000 |
| parents | |
| children | a8de96a8b8eb |
| files | qiime2__feature_table__heatmap.xml test-data/merge.test0.feature-table1.qza test-data/merge.test0.feature-table2.qza test-data/merge.test1.feature-table1.qza test-data/merge.test1.feature-table2.qza test-data/merge.test1.feature-table3.qza |
| diffstat | 6 files changed, 338 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__heatmap.xml Mon Aug 29 19:56:45 2022 +0000 @@ -0,0 +1,338 @@ +<?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 feature-table heatmap" id="qiime2__feature_table__heatmap" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Generate a heatmap representation of a feature table</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version feature_table</version_command> + <command detect_errors="aggressive">q2galaxy run feature_table 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 to visualize."> + <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> + <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] Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values."> + <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] Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`='sample', features will be sorted by the metadata values."> + <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="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."/> + <conditional name="__q2galaxy__GUI__conditional__title__" label="title: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="title: Str" help="[optional] Optional custom plot title."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="title" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="title" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <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">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" selected="true">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" selected="true">both</option> + <option value="features">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="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: feature-table heatmap +============================== +Generate a heatmap representation of a feature table + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Generate a heatmap representation of a feature table with optional clustering on both the sample and feature axes. + +Tip: To generate a heatmap containing taxonomic annotations, use `qiime taxa collapse` to collapse the feature table at the desired taxonomic level. + + +| + +</help> + <citations> + <citation type="doi">10.1109/MCSE.2007.55</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>