Mercurial > repos > q2d2 > qiime2__alignment__mafft_add

changeset 9:3c8af46b66c9 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 36ec48f8c55799a0c963733df13da30f19b1bdf3
author q2d2
date Wed, 28 Jan 2026 16:10:56 +0000
parents d32cbac620eb
children
files qiime2__alignment__mafft_add.xml
diffstat 1 files changed, 22 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/qiime2__alignment__mafft_add.xml	Sat Nov 01 17:07:02 2025 +0000
+++ b/qiime2__alignment__mafft_add.xml	Wed Jan 28 16:10:56 2026 +0000
@@ -1,22 +1,22 @@
 <?xml version='1.0' encoding='utf-8'?>
 <!--
-Copyright (c) 2025, QIIME 2 development team.
+Copyright (c) 2026, 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: 2025.10.0)
+    q2galaxy (version: 2026.1.0)
 for:
-    qiime2 (version: 2025.10.0)
+    qiime2 (version: 2026.1.0)
 -->
-<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2026.1.0+q2galaxy.2026.1.0" profile="22.05" license="BSD-3-Clause">
     <description>Add sequences to multiple sequence alignment with MAFFT.</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
+        <container type="docker">quay.io/qiime2/amplicon:2026.1</container>
     </requirements>
     <version_command>q2galaxy version alignment</version_command>
     <command detect_errors="exit_code">q2galaxy run alignment mafft_add '$inputs'</command>
@@ -24,23 +24,35 @@
         <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
-        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to which sequences should be added.">
+        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]¹ | FeatureData[AlignedProteinSequence]²" help="[required]  The alignment to which sequences should be added.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+                <filter type="add_value" value="FeatureData[AlignedProteinSequence]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedProteinSequence]', 'FeatureData[AlignedSequence]']</validator>
         </param>
-        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be added.">
+        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]¹ | FeatureData[ProteinSequence]²" help="[required]  The sequences to be added.">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureData[Sequence]"/>
+                <filter type="add_value" value="FeatureData[ProteinSequence]"/>
             </options>
-            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[ProteinSequence]', 'FeatureData[Sequence]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <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="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 1,000,000. Disabled by default."/>
             <param name="addfragments" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="addfragments: Bool" help="[default: No]  Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used."/>
             <param name="keeplength" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="keeplength: Bool" help="[default: No]  If selected, the alignment length will be unchanged. Any added sequence that would otherwise introduce new insertions into the alignment, will have those insertions deleted, to preserve original alignment length."/>
             <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="strategy" type="select" label="strategy: Str % Choices('auto', 'genafpair', 'globalpair', 'localpair', 'nofft')">
+                <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
+                <option value="auto">auto</option>
+                <option value="genafpair">genafpair</option>
+                <option value="globalpair">globalpair</option>
+                <option value="localpair">localpair</option>
+                <option value="nofft">nofft</option>
+            </param>
+            <param name="maxiterate" type="integer" min="0" optional="true" label="maxiterate: Int % Range(0, None)" help="[optional]  Specifies how many iterative refinement cycles are performed after the initial progressive alignment. By default, no iterative refinement is performed."/>
+            <param name="retree" type="integer" min="0" optional="true" label="retree: Int % Range(0, None)" help="[optional]  Specifies the number of times the guide tree is rebuilt during the progressive stage. Typically, tree topology stabilizes after 2-3 iterations and higher values rarely improves alignment quality enough to justify the extra computation."/>
         </section>
     </inputs>
     <outputs>