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changeset 0:34ca8ab70ecb draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__gneiss commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:06:13 +0000
parents
children ec24bc691af1
files qiime2__gneiss__dendrogram_heatmap.xml test-data/.gitkeep
diffstat 1 files changed, 178 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__gneiss__dendrogram_heatmap.xml	Mon Aug 29 20:06:13 2022 +0000
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+<?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 gneiss dendrogram-heatmap" id="qiime2__gneiss__dendrogram_heatmap" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Dendrogram heatmap.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version gneiss</version_command>
+    <command detect_errors="aggressive">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>