# HG changeset patch
# User q2d2
# Date 1661801521 0
# Node ID b9c031cf3ea5abb1ff57afaee6e9c58c27e79a58

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r b9c031cf3ea5 qiime2__diversity__beta.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__diversity__beta.xml	Mon Aug 29 19:32:01 2022 +0000
@@ -0,0 +1,102 @@
+<?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 diversity beta" id="qiime2__diversity__beta" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Beta diversity</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version diversity</version_command>
+    <command detect_errors="aggressive">q2galaxy run diversity beta '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required]  The feature table containing the samples over which beta diversity should be computed.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator>
+        </param>
+        <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'jensenshannon', 'kulsinski', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule')">
+            <option value="__q2galaxy__::literal::None">Selection required</option>
+            <option value="aitchison">aitchison</option>
+            <option value="braycurtis">braycurtis</option>
+            <option value="canberra">canberra</option>
+            <option value="canberra_adkins">canberra_adkins</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="jensenshannon">jensenshannon</option>
+            <option value="kulsinski">kulsinski</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>
+            <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1]  A pseudocount to handle zeros for compositional metrics.  This is ignored for other metrics."/>
+            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host.">
+                    <option value="auto">auto (Str)</option>
+                    <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option>
+                </param>
+                <when value="auto">
+                    <param name="n_jobs" type="hidden" value="auto"/>
+                </when>
+                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
+                    <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1]  The number of concurrent jobs to use in performing this calculation. May not exceed the number of available physical cores. If n_jobs = 'auto', one job will be launched for each identified CPU core on the host."/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="distance_matrix" format="qza" label="${tool.name} on ${on_string}: distance_matrix.qza" from_work_dir="distance_matrix.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: diversity beta
+=======================
+Beta diversity
+
+
+Outputs:
+--------
+:distance_matrix.qza: The resulting distance matrix.
+
+|  
+
+Description:
+------------
+Computes a user-specified beta diversity metric for all pairs of samples in a feature table.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r b9c031cf3ea5 test-data/.gitkeep