# HG changeset patch
# User q2d2
# Date 1714078860 0
# Node ID a1166fa9986e11acf6915aa7c1ae81a43eb12f79
# Parent  fcbeb4dc4b81901f3bb9b24de03d7c90f9809c7a
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r fcbeb4dc4b81 -r a1166fa9986e qiime2__diversity_lib__beta_phylogenetic_passthrough.xml
--- a/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml	Thu Jun 08 19:38:53 2023 +0000
+++ b/qiime2__diversity_lib__beta_phylogenetic_passthrough.xml	Thu Apr 25 21:01:00 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-phylogenetic-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 diversity-lib beta-phylogenetic-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Beta Phylogenetic Passthrough</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_phylogenetic_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.">
@@ -42,18 +42,6 @@
             <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">
-            <conditional name="__q2galaxy__GUI__conditional__threads__">
-                <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread 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="threads" type="hidden" value="auto"/>
-                </when>
-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
-                    <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1]  The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/>
-                </when>
-            </conditional>
             <param name="variance_adjusted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="variance_adjusted: Bool" help="[default: No]  Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation."/>
             <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional]  This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized."/>
             <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No]  In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/>
@@ -79,10 +67,6 @@
             <param name="table" value="beta_phylogenetic_passthrough.test1.feature-table.qza" ftype="qza"/>
             <param name="phylogeny" value="beta_phylogenetic_passthrough.test1.phylogeny.qza" ftype="qza"/>
             <param name="metric" value="weighted_normalized_unifrac"/>
-            <conditional name="__q2galaxy__GUI__conditional__threads__">
-                <param name="__q2galaxy__GUI__select__" value="__q2galaxy__::control::Int X Range(1__comma__ None)"/>
-                <param name="threads" 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">
@@ -95,10 +79,6 @@
             <param name="table" value="beta_phylogenetic_passthrough.test2.feature-table.qza" ftype="qza"/>
             <param name="phylogeny" value="beta_phylogenetic_passthrough.test2.phylogeny.qza" ftype="qza"/>
             <param name="metric" value="weighted_normalized_unifrac"/>
-            <conditional name="__q2galaxy__GUI__conditional__threads__">
-                <param name="__q2galaxy__GUI__select__" value="auto"/>
-                <param name="threads" 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">
@@ -111,10 +91,6 @@
             <param name="table" value="beta_phylogenetic_passthrough.test3.feature-table.qza" ftype="qza"/>
             <param name="phylogeny" value="beta_phylogenetic_passthrough.test3.phylogeny.qza" ftype="qza"/>
             <param name="metric" value="weighted_normalized_unifrac"/>
-            <conditional name="__q2galaxy__GUI__conditional__threads__">
-                <param name="__q2galaxy__GUI__select__" value="auto"/>
-                <param name="threads" value="auto"/>
-            </conditional>
             <param name="bypass_tips" value="__q2galaxy__::literal::True"/>
             <output name="distance_matrix" ftype="qza">
                 <assert_contents>
@@ -128,10 +104,6 @@
             <param name="table" value="beta_phylogenetic_passthrough.test4.feature-table.qza" ftype="qza"/>
             <param name="phylogeny" value="beta_phylogenetic_passthrough.test4.phylogeny.qza" ftype="qza"/>
             <param name="metric" value="weighted_unifrac"/>
-            <conditional name="__q2galaxy__GUI__conditional__threads__">
-                <param name="__q2galaxy__GUI__select__" value="auto"/>
-                <param name="threads" value="auto"/>
-            </conditional>
             <param name="variance_adjusted" value="__q2galaxy__::literal::True"/>
             <output name="distance_matrix" ftype="qza">
                 <assert_contents>
@@ -212,10 +184,6 @@
  #. Set *"table"* to ``#: feature-table.qza``
  #. Set *"phylogeny"* to ``#: phylogeny.qza``
  #. Set *"metric"* to ``weighted_normalized_unifrac``
- #. Expand the ``additional options`` section
-
-    - Leave *"threads"* 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:
@@ -236,10 +204,6 @@
  #. Set *"table"* to ``#: feature-table.qza``
  #. Set *"phylogeny"* to ``#: phylogeny.qza``
  #. Set *"metric"* to ``weighted_normalized_unifrac``
- #. Expand the ``additional options`` section
-
-    - Set *"threads"* 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:
@@ -263,8 +227,7 @@
  #. Set *"metric"* to ``weighted_normalized_unifrac``
  #. Expand the ``additional options`` section
 
-    #. Set *"threads"* to ``auto``
-    #. Set *"bypass_tips"* to ``Yes``
+    - Set *"bypass_tips"* to ``Yes``
 
  #. Press the ``Execute`` button.
 
@@ -289,8 +252,7 @@
  #. Set *"metric"* to ``weighted_unifrac``
  #. Expand the ``additional options`` section
 
-    #. Set *"threads"* to ``auto``
-    #. Set *"variance_adjusted"* to ``Yes``
+    - Set *"variance_adjusted"* to ``Yes``
 
  #. Press the ``Execute`` button.
 
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