# HG changeset patch
# User q2d2
# Date 1762018095 0
# Node ID ed4ab852f3508b44846e759cd654558134392b5a
# Parent  0991e282a78941a9e198f121b95fea605249bb0e
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r 0991e282a789 -r ed4ab852f350 qiime2__phylogeny__align_to_tree_mafft_iqtree.xml
--- a/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml	Tue Jul 15 22:02:42 2025 +0000
+++ b/qiime2__phylogeny__align_to_tree_mafft_iqtree.xml	Sat Nov 01 17:28:15 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.7.0)
+    q2galaxy (version: 2025.10.0)
 for:
-    qiime2 (version: 2025.7.0)
+    qiime2 (version: 2025.10.0)
 -->
-<tool name="qiime2 phylogeny align-to-tree-mafft-iqtree" id="qiime2__phylogeny__align_to_tree_mafft_iqtree" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 phylogeny align-to-tree-mafft-iqtree" id="qiime2__phylogeny__align_to_tree_mafft_iqtree" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Build a phylogenetic tree using iqtree and mafft alignment.</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
     </requirements>
     <version_command>q2galaxy version phylogeny</version_command>
     <command detect_errors="exit_code">q2galaxy run phylogeny align_to_tree_mafft_iqtree '$inputs'</command>
@@ -33,6 +33,8 @@
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <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."/>
+            <param name="large" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="large: Bool" help="[default: No]  This flag is required when aligning very large datasets that do not otherwise fit into memory. Temporary data is then stored in files, instead of RAM. The temporary files are stored in the QIIME 2 Artifact cache. The default location of the cache is $TMP/qiime2/&lt;uname&gt;."/>
             <param name="substitution_model" type="select" label="substitution_model: Str % Choices('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST')">
                 <option value="JC">JC</option>
                 <option value="JC+I">JC+I</option>
diff -r 0991e282a789 -r ed4ab852f350 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