# HG changeset patch
# User q2d2
# Date 1762018087 0
# Node ID e534f88ab7bd426775b9ce3bf48c1abcaefcbf37
# Parent  94f6ae67f9423e68a4dd66cf015fc202a38ac1e7
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r 94f6ae67f942 -r e534f88ab7bd qiime2__phylogeny__align_to_tree_mafft_raxml.xml
--- a/qiime2__phylogeny__align_to_tree_mafft_raxml.xml	Tue Jul 15 22:03:03 2025 +0000
+++ b/qiime2__phylogeny__align_to_tree_mafft_raxml.xml	Sat Nov 01 17:28:07 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-raxml" id="qiime2__phylogeny__align_to_tree_mafft_raxml" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 phylogeny align-to-tree-mafft-raxml" id="qiime2__phylogeny__align_to_tree_mafft_raxml" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Build a phylogenetic tree using raxml 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_raxml '$inputs'</command>
@@ -34,6 +34,7 @@
             <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. NOTE: if using this option, it is recomended that only the CAT-based substitution models of RAxML be considered for this pipeline."/>
+            <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 --use-cache flag specifies the storage location of the temporary files created. By default, $TMP/qiime2/ is used."/>
             <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio">
                 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
                 <option value="GTRGAMMAI">GTRGAMMAI</option>
diff -r 94f6ae67f942 -r e534f88ab7bd 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