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+++ b/table-union.xml	Mon Dec 08 15:03:06 2025 +0000
@@ -0,0 +1,99 @@
+<tool id="table-union" name="Table Union: Merge tabular datasets" version="0.1.0">
+    <description>by combining their rows and unionizing columns</description>
+    <requirements>
+        <container type="docker">cfsanbiostatistics/tableops:latest</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    	#if $input_type.source_select == 'two'
+    	#set tables=($table_1, $table_2)
+    	#else
+    	#set tables=$input_type.tables
+    	#end if
+        python $__tool_directory__/table-union.py $adv.union $adv.tuple_mode
+        #for $table in $tables
+            $table
+        #end for
+        > $combined_table
+    ]]></command>
+    <inputs>
+    	<conditional name="input_type">
+    		<param name="source_select" type="select" label="Mode">
+    			<option value="two">Combine two tables</option>
+    			<option value="collection">Combine a collection of tables</option>
+    		</param>
+    		<when value="collection">
+       			<param name="tables" type="data_collection" format="tabular,tsv" collection_type="list" optional="true" />
+       		</when>
+       		<when value="two">
+       			<param name="table_1" type="data" format="tabular,tsv" optional="true" />
+       			<param name="table_2" type="data" format="tabular,tsv" optional="true"/>
+       		</when>
+        </conditional>
+        <!-- Advanced options, click to show -->
+        <section name="adv" title="Advanced options">
+            <param name="union" type="boolean" label="Attempt to unionize on an autodetected key column" checked="false" truevalue="--unionize" falsevalue="" />
+            <param name="tuple_mode" type="boolean" label="For tables with inconsistent headers - unionize by column order instead of column " checked="false" truevalue="--tuple" falsevalue="" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="combined_table" format="tsv" label="Combined table" />
+    </outputs>
+
+    <tests>
+        <test>
+        	<conditional name="input_type">
+        		<param name="source_select" value="collection" />
+            
+            <param name="tables">
+                <collection type="list">
+                    <element name="table_1" value="dingbat.tsv" />
+                    <element name="table_2" value="loki.tsv" />
+                </collection>
+            </param>
+            </conditional>
+            <section name="adv">
+            <param name="union" value="true" />
+            </section>
+            <output name="combined_table" value="combined.tsv" />
+        </test>
+        <test>
+        	<conditional name="input_type">
+        		<param name="source_select" value="two" />
+            
+        	<param name="table_1" value="dingbat.tsv" />
+        	<param name="table_2" value="loki.tsv" />
+            </conditional>
+            <section name="adv">
+            <param name="union" value="false" />
+            </section>
+        	<output name="combined_table" value="no_union.tsv" />
+        </test>
+        <test>
+        	<conditional name="input_type">
+        		<param name="source_select" value="two" />
+            
+        	<param name="table_1" value="dingbat.tsv" />
+        	<param name="table_2" value="loki.tsv" />
+            </conditional>
+            <section name="adv">
+            <param name="tuple_mode" value="true" />
+            </section>  
+        	<output name="combined_table" value="tuple.tsv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Concatenate a collection of TSV files wile preserving and unionizing headers.
+    ]]></help>
+
+    <citations>
+            <citation type="bibtex">
+@misc{githubsometool,
+  author = {Payne, Justin},
+  year = {2022},
+  title = {tableops},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CFSAN-Biostatistics/table-ops},
+}</citation>
+    </citations>
+</tool>
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