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+++ b/qiime2__feature_table__merge.xml	Mon Aug 29 20:00:50 2022 +0000
@@ -0,0 +1,109 @@
+<?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 feature-table merge" id="qiime2__feature_table__merge" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
+    <description>Combine multiple tables</description>
+    <requirements>
+        <container type="docker">quay.io/qiime2/core:2022.8</container>
+    </requirements>
+    <version_command>q2galaxy version feature_table</version_command>
+    <command detect_errors="aggressive">q2galaxy run feature_table merge '$inputs'</command>
+    <configfiles>
+        <inputs name="inputs" data_style="paths"/>
+    </configfiles>
+    <inputs>
+        <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]¹ | FeatureTable[RelativeFrequency]²]" help="[required]  The collection of feature tables to be merged." multiple="true">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+                <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
+            </options>
+        </param>
+        <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
+            <param name="overlap_method" type="select" label="overlap_method: Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample', 'sum')¹ | Str % Choices('average', 'error_on_overlapping_feature', 'error_on_overlapping_sample')²" help="[default: 'error_on_overlapping_sample']  Method for handling overlapping ids.">
+                <option value="average">average (Str)</option>
+                <option value="error_on_overlapping_feature">error_on_overlapping_feature (Str)</option>
+                <option value="error_on_overlapping_sample" selected="true">error_on_overlapping_sample (Str)</option>
+                <option value="sum">sum (Str)</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="merged_table" format="qza" label="${tool.name} on ${on_string}: merged_table.qza" from_work_dir="merged_table.qza"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tables" value="merge.test0.feature-table1.qza,merge.test0.feature-table2.qza" ftype="qza"/>
+            <output name="merged_table" ftype="qza"/>
+        </test>
+        <test>
+            <param name="tables" value="merge.test1.feature-table1.qza,merge.test1.feature-table2.qza,merge.test1.feature-table3.qza" ftype="qza"/>
+            <conditional name="__q2galaxy__GUI__conditional__overlap_method__">
+                <param name="__q2galaxy__GUI__select__" value="sum"/>
+                <param name="overlap_method" value="sum"/>
+            </conditional>
+            <output name="merged_table" ftype="qza"/>
+        </test>
+    </tests>
+    <help>
+QIIME 2: feature-table merge
+============================
+Combine multiple tables
+
+
+Outputs:
+--------
+:merged_table.qza: The resulting merged feature table.
+
+|  
+
+Description:
+------------
+Combines feature tables using the `overlap_method` provided.
+
+Examples:
+---------
+
+basic
+*****
+Using the ``qiime2 feature-table merge`` tool:
+ #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
+
+    #. ``#: feature-table1.qza``
+    #. ``#: feature-table2.qza``
+
+ #. Press the ``Execute`` button.
+
+
+three_tables
+************
+Using the ``qiime2 feature-table merge`` tool:
+ #. For *"tables"*, use ctrl-(or command)-click to select the following inputs:
+
+    #. ``#: feature-table1.qza``
+    #. ``#: feature-table2.qza``
+    #. ``#: feature-table3.qza``
+
+ #. Expand the ``additional options`` section
+
+    - Set *"overlap_method"* to ``sum``
+
+ #. Press the ``Execute`` button.
+
+
+
+|  
+
+</help>
+    <citations>
+        <citation type="doi">10.1038/s41587-019-0209-9</citation>
+    </citations>
+</tool>

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