# HG changeset patch
# User q2d2
# Date 1661800725 0
# Node ID 631f37aab4647b9a5c87cd2242b484d2e37a20d8

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

diff -r 000000000000 -r 631f37aab464 qiime2__alignment__mafft_add.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__alignment__mafft_add.xml	Mon Aug 29 19:18:45 2022 +0000
@@ -0,0 +1,81 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+Copyright (c) 2022, 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: 2022.8.1)
+for:
+    qiime2 (version: 2022.8.1)
+-->
+<tool name="qiime2 alignment mafft-add" id="qiime2__alignment__mafft_add" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Add sequences to multiple sequence alignment with MAFFT.</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version alignment</version_command>
+    <command detect_errors="aggressive">q2galaxy run alignment mafft_add '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required]  The alignment to which sequences should be added.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[AlignedSequence]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator>
+        </param>
+        <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]  The sequences to be added.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureData[Sequence]"/>
+            </options>
+            <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)">
+                    <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)"/>
+                </when>
+            </conditional>
+            <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="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."/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="expanded_alignment" format="qza" label="${tool.name} on ${on_string}: expanded_alignment.qza" from_work_dir="expanded_alignment.qza"/>
+    </outputs>
+    <tests/>
+    <help>
+QIIME 2: alignment mafft-add
+============================
+Add sequences to multiple sequence alignment with MAFFT.
+
+
+Outputs:
+--------
+:expanded_alignment.qza: Alignment containing the provided aligned and unaligned sequences.
+
+|  
+
+Description:
+------------
+Add new sequences to an existing alignment with MAFFT.
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1093/molbev/mst010</citation>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 631f37aab464 test-data/.gitkeep