# HG changeset patch
# User q2d2
# Date 1714078625 0
# Node ID 76e136962089228e5a0742a9195241b53aac3aaa
# Parent  9d29f6a334e52193f29d7a442fd48169481166d5
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 9d29f6a334e5 -r 76e136962089 qiime2__diversity__core_metrics_phylogenetic.xml
--- a/qiime2__diversity__core_metrics_phylogenetic.xml	Thu Jun 08 19:37:36 2023 +0000
+++ b/qiime2__diversity__core_metrics_phylogenetic.xml	Thu Apr 25 20:57:05 2024 +0000
@@ -1,24 +1,24 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2023, QIIME 2 development team.
+Copyright (c) 2024, 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: 2023.5.0)
+    q2galaxy (version: 2024.2.1)
 for:
-    qiime2 (version: 2023.5.1)
+    qiime2 (version: 2024.2.0)
 -->
-<tool name="qiime2 diversity core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 diversity core-metrics-phylogenetic" id="qiime2__diversity__core_metrics_phylogenetic" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Core diversity metrics (phylogenetic and non-phylogenetic)</description>
     <requirements>
-        <container type="docker">quay.io/qiime2/core:2023.5</container>
+        <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
     </requirements>
     <version_command>q2galaxy version diversity</version_command>
     <command detect_errors="exit_code">q2galaxy run diversity core_metrics_phylogenetic '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required]  The feature table containing the samples over which diversity metrics should be computed.">
@@ -50,18 +50,7 @@
         </repeat>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <param name="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No]  Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/>
-            <conditional name="__q2galaxy__GUI__conditional__n_jobs_or_threads__">
-                <param name="__q2galaxy__GUI__select__" type="select" label="n_jobs_or_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created 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_or_threads" type="hidden" value="auto"/>
-                </when>
-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
-                    <param name="n_jobs_or_threads" type="integer" min="1" value="1" label="n_jobs_or_threads: Int % Range(1, None)" help="[default: 1]  [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created for each identified CPU core on the host."/>
-                </when>
-            </conditional>
+            <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No]  If set to `True` samples and features without metadata are included by setting all metadata values to: &quot;This element has no metadata&quot;. By default an exception will be raised if missing elements are encountered. Note, this flag only takes effect if there is at least one overlapping element."/>
         </section>
     </inputs>
     <outputs>
diff -r 9d29f6a334e5 -r 76e136962089 test-data/alpha_correlation.test0.alpha-div-faith-pd.qza
Binary file test-data/alpha_correlation.test0.alpha-div-faith-pd.qza has changed
diff -r 9d29f6a334e5 -r 76e136962089 test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza
Binary file test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza has changed