# HG changeset patch
# User q2d2
# Date 1714079850 0
# Node ID e226dcac1ec8b2f946cdd698e7551535bd8801cb
# Parent  2a9461620d5e501fc37475ca6f373c6576f2bd18
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 2a9461620d5e -r e226dcac1ec8 qiime2__phylogeny__align_to_tree_mafft_fasttree.xml
--- a/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml	Thu Jun 08 19:50:15 2023 +0000
+++ b/qiime2__phylogeny__align_to_tree_mafft_fasttree.xml	Thu Apr 25 21:17:30 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 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 phylogeny align-to-tree-mafft-fasttree" id="qiime2__phylogeny__align_to_tree_mafft_fasttree" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Build a phylogenetic tree using fasttree and mafft alignment</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 phylogeny</version_command>
     <command detect_errors="exit_code">q2galaxy run phylogeny align_to_tree_mafft_fasttree '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
         <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be used for creating a fasttree based rooted phylogenetic tree.">
@@ -28,18 +28,6 @@
             <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <conditional name="__q2galaxy__GUI__conditional__n_threads__">
-                <param name="__q2galaxy__GUI__select__" type="select" label="n_threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree.">
-                    <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_threads" type="hidden" value="auto"/>
-                </when>
-                <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
-                    <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1]  The number of threads. (Use `auto` to automatically use all available cores) This value is used when aligning the sequences and creating the tree with fasttree."/>
-                </when>
-            </conditional>
             <param name="mask_max_gap_frequency" type="float" min="0" max="1" value="1.0" label="mask_max_gap_frequency: Float % Range(0, 1, inclusive_end=True)" help="[default: 1.0]  The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns  regardless of gap character frequency. This value is used when masking the aligned sequences."/>
             <param name="mask_min_conservation" type="float" min="0" max="1" value="0.4" label="mask_min_conservation: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.4]  The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of  0.4 is provided, a column will only be retained  if it contains at least one character that is present in at least 40% of the sequences. This value is used when masking the aligned sequences."/>
             <param name="parttree" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="parttree: Bool" help="[default: No]  This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default."/>
diff -r 2a9461620d5e -r e226dcac1ec8 test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza
Binary file test-data/align_to_tree_mafft_fasttree.test0.rep-seqs.qza has changed