# HG changeset patch
# User q2d2
# Date 1714079487 0
# Node ID 6bad55f4a31004a4eaae1e0af7fdec1c731f9b4c
# Parent  4c2751c8cc0da4981c8d5f223825318ed221975f
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e

diff -r 4c2751c8cc0d -r 6bad55f4a310 qiime2__feature_table__merge.xml
--- a/qiime2__feature_table__merge.xml	Thu Jun 08 19:46:38 2023 +0000
+++ b/qiime2__feature_table__merge.xml	Thu Apr 25 21:11:27 2024 +0000
@@ -1,38 +1,40 @@
 <?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 feature-table merge" id="qiime2__feature_table__merge" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 feature-table merge" id="qiime2__feature_table__merge" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
     <description>Combine multiple tables</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 feature_table</version_command>
     <command detect_errors="exit_code">q2galaxy run feature_table merge '$inputs'</command>
     <configfiles>
-        <inputs name="inputs" data_style="paths"/>
+        <inputs name="inputs" data_style="staging_path_and_source_path"/>
     </configfiles>
     <inputs>
-        <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]²]" help="[required]  The collection of feature tables to be merged." multiple="true">
+        <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]² | FeatureTable[PresenceAbsence]³]" help="[required]  The collection of feature tables to be merged." multiple="true">
             <options options_filter_attribute="metadata.semantic_type">
                 <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+                <filter type="add_value" value="FeatureTable[PresenceAbsence]"/>
             </options>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
-            <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')²" help="[default: 'error_on_overlapping_sample']  Method for handling overlapping ids.">
+            <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')² | Str % Choices('error_on_overlapping_feature', 'error_on_overlapping_sample', 'union')³" help="[default: 'error_on_overlapping_sample']  Method for handling overlapping ids.">
                 <option value="average">average (Str)</option>
                 <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option>
                 <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option>
                 <option value="sum">sum (Str)</option>
+                <option value="union">union (Str)</option>
             </param>
         </section>
     </inputs>
diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_features.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_features_conditionally.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test1.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test2.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test3.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test4.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test5.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/filter_samples.test6.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/group.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge.test0.feature-table1.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge.test0.feature-table2.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge.test1.feature-table1.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge.test1.feature-table2.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge.test1.feature-table3.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge_seqs.test0.seqs1.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge_seqs.test0.seqs2.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge_taxa.test0.tax1.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/merge_taxa.test0.tax2.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/summarize.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/summarize_plus.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_feature_frequencies.test0.feature-table.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_seqs.test0.rep-seqs.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_seqs.test2.multi-taxonomy/.order
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tabulate_seqs.test2.multi-taxonomy/.order	Thu Apr 25 21:11:27 2024 +0000
@@ -0,0 +1,2 @@
+GG1
+GG2
diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_seqs.test2.multi-taxonomy/GG1.qza
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diff -r 4c2751c8cc0d -r 6bad55f4a310 test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza
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