# HG changeset patch
# User q2d2
# Date 1714079018 0
# Node ID 0969c54eddc652a86229c1e8a54f42734a1565a2
# Parent  38a55b074008234b248d4e66e9fede3ac7a78a31
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 38a55b074008 -r 0969c54eddc6 qiime2__diversity_lib__beta_passthrough.xml
--- a/qiime2__diversity_lib__beta_passthrough.xml	Thu Jun 08 19:41:21 2023 +0000
+++ b/qiime2__diversity_lib__beta_passthrough.xml	Thu Apr 25 21:03:38 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-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 diversity-lib beta-passthrough" id="qiime2__diversity_lib__beta_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Beta Passthrough (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_lib</version_command>
     <command detect_errors="exit_code">q2galaxy run diversity_lib beta_passthrough '$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 beta diversity should be computed.">
@@ -54,18 +54,6 @@
         </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 non-compositional 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>
@@ -86,10 +74,6 @@
         <test>
             <param name="table" value="beta_passthrough.test1.feature-table.qza" ftype="qza"/>
             <param name="metric" value="kulsinski"/>
-            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
-                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
-                <param name="n_jobs" value="1"/>
-            </conditional>
             <output name="distance_matrix" ftype="qza">
                 <assert_contents>
                     <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
@@ -101,10 +85,6 @@
         <test>
             <param name="table" value="beta_passthrough.test2.feature-table.qza" ftype="qza"/>
             <param name="metric" value="aitchison"/>
-            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
-                <param name="__q2galaxy__GUI__select__" value="auto"/>
-                <param name="n_jobs" value="auto"/>
-            </conditional>
             <output name="distance_matrix" ftype="qza">
                 <assert_contents>
                     <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
@@ -117,10 +97,6 @@
             <param name="table" value="beta_passthrough.test3.feature-table.qza" ftype="qza"/>
             <param name="metric" value="aitchison"/>
             <param name="pseudocount" value="5"/>
-            <conditional name="__q2galaxy__GUI__conditional__n_jobs__">
-                <param name="__q2galaxy__GUI__select__" value="auto"/>
-                <param name="n_jobs" value="auto"/>
-            </conditional>
             <output name="distance_matrix" ftype="qza">
                 <assert_contents>
                     <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
@@ -173,10 +149,6 @@
 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
  #. Set *"table"* to ``#: feature-table.qza``
  #. Set *"metric"* to ``kulsinski``
- #. Expand the ``additional options`` section
-
-    - Leave *"n_jobs"* as its default value of ``1``
-
  #. Press the ``Execute`` button.
 
 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
@@ -197,10 +169,6 @@
 Using the ``qiime2 diversity-lib beta-passthrough`` tool:
  #. Set *"table"* to ``#: feature-table.qza``
  #. Set *"metric"* to ``aitchison``
- #. Expand the ``additional options`` section
-
-    - Set *"n_jobs"* to ``auto``
-
  #. Press the ``Execute`` button.
 
 Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:
@@ -222,8 +190,7 @@
  #. Set *"metric"* to ``aitchison``
  #. Expand the ``additional options`` section
 
-    #. Set *"pseudocount"* to ``5``
-    #. Set *"n_jobs"* to ``auto``
+    - Set *"pseudocount"* to ``5``
 
  #. Press the ``Execute`` button.
 
diff -r 38a55b074008 -r 0969c54eddc6 test-data/alpha_passthrough.test0.feature-table.qza
Binary file test-data/alpha_passthrough.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_passthrough.test0.feature-table.qza
Binary file test-data/beta_passthrough.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_passthrough.test1.feature-table.qza
Binary file test-data/beta_passthrough.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_passthrough.test2.feature-table.qza
Binary file test-data/beta_passthrough.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_passthrough.test3.feature-table.qza
Binary file test-data/beta_passthrough.test3.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test0.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test1.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test2.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test3.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test4.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test5.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test6.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/bray_curtis.test0.feature-table.qza
Binary file test-data/bray_curtis.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/bray_curtis.test1.feature-table.qza
Binary file test-data/bray_curtis.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/bray_curtis.test2.feature-table.qza
Binary file test-data/bray_curtis.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/faith_pd.test0.feature-table.qza
Binary file test-data/faith_pd.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/faith_pd.test0.phylogeny.qza
Binary file test-data/faith_pd.test0.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/jaccard.test0.feature-table.qza
Binary file test-data/jaccard.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/jaccard.test1.feature-table.qza
Binary file test-data/jaccard.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/jaccard.test2.feature-table.qza
Binary file test-data/jaccard.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/observed_features.test0.feature-table.qza
Binary file test-data/observed_features.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/pielou_evenness.test0.feature-table.qza
Binary file test-data/pielou_evenness.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/pielou_evenness.test1.feature-table.qza
Binary file test-data/pielou_evenness.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/shannon_entropy.test0.feature-table.qza
Binary file test-data/shannon_entropy.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/shannon_entropy.test1.feature-table.qza
Binary file test-data/shannon_entropy.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test0.feature-table.qza
Binary file test-data/unweighted_unifrac.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test0.phylogeny.qza
Binary file test-data/unweighted_unifrac.test0.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test1.feature-table.qza
Binary file test-data/unweighted_unifrac.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test1.phylogeny.qza
Binary file test-data/unweighted_unifrac.test1.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test2.feature-table.qza
Binary file test-data/unweighted_unifrac.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test2.phylogeny.qza
Binary file test-data/unweighted_unifrac.test2.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test3.feature-table.qza
Binary file test-data/unweighted_unifrac.test3.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/unweighted_unifrac.test3.phylogeny.qza
Binary file test-data/unweighted_unifrac.test3.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test0.feature-table.qza
Binary file test-data/weighted_unifrac.test0.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test0.phylogeny.qza
Binary file test-data/weighted_unifrac.test0.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test1.feature-table.qza
Binary file test-data/weighted_unifrac.test1.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test1.phylogeny.qza
Binary file test-data/weighted_unifrac.test1.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test2.feature-table.qza
Binary file test-data/weighted_unifrac.test2.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test2.phylogeny.qza
Binary file test-data/weighted_unifrac.test2.phylogeny.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test3.feature-table.qza
Binary file test-data/weighted_unifrac.test3.feature-table.qza has changed
diff -r 38a55b074008 -r 0969c54eddc6 test-data/weighted_unifrac.test3.phylogeny.qza
Binary file test-data/weighted_unifrac.test3.phylogeny.qza has changed