# HG changeset patch
# User q2d2
# Date 1661802539 0
# Node ID 72079afffe4cfb3fa444dfebc5bfcd5175094bbf

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 72079afffe4c qiime2__emperor__biplot.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__emperor__biplot.xml	Mon Aug 29 19:48:59 2022 +0000
@@ -0,0 +1,93 @@
+<?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 emperor biplot" id="qiime2__emperor__biplot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version emperor</version_command>
+    <command detect_errors="aggressive">q2galaxy run emperor biplot '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="biplot" type="data" format="qza" label="biplot: PCoAResults % Properties('biplot')" help="[required]  The principal coordinates matrix to be plotted.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="PCoAResults % Properties('biplot')"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ["PCoAResults % Properties('biplot')"]</validator>
+        </param>
+        <repeat name="sample_metadata" min="1" help="[required]  The sample metadata" title="sample_metadata: Metadata">
+            <conditional name="__q2galaxy__GUI__conditional__sample_metadata__">
+                <param name="type" type="select" label="sample_metadata: Metadata">
+                    <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"/>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                </when>
+            </conditional>
+        </repeat>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <repeat name="feature_metadata" help="[optional]  The feature metadata (useful to manipulate the arrows in the plot)." title="feature_metadata: Metadata">
+                <conditional name="__q2galaxy__GUI__conditional__feature_metadata__">
+                    <param name="type" type="select" label="feature_metadata: Metadata">
+                        <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"/>
+                    </when>
+                    <when value="qza">
+                        <param name="source" type="data" format="qza" label="Metadata Source"/>
+                    </when>
+                </conditional>
+            </repeat>
+            <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No]  This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: &quot;This sample has no metadata&quot;. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/>
+            <param name="invert" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="invert: Bool" help="[default: No]  If specified, the point and arrow coordinates will be swapped."/>
+            <param name="number_of_features" type="integer" min="1" value="5" label="number_of_features: Int % Range(1, None)" help="[default: 5]  The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin)."/>
+        </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: emperor biplot
+=======================
+Visualize and Interact with Principal Coordinates Analysis Biplot
+
+
+Outputs:
+--------
+:visualization.qzv: &lt;no description&gt;
+
+|  
+
+Description:
+------------
+Generates an interactive ordination biplot where the user can visually integrate sample and feature metadata. Vectors representing the n most important features are then plotted in the emperor visualization (5 largest, by default).
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1186/2047-217X-2-16</citation>
+        <citation type="doi">10.1016/j.chom.2016.12.009</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 72079afffe4c test-data/.gitkeep