--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/join_nucmer/join_nucmer.xml	Thu Jul 23 12:54:02 2020 +0000
@@ -0,0 +1,34 @@
+<tool id="join_nucmer" name="join_nucmer" version="">
+  <description></description>
+  <command>
+ <![CDATA[
+	perl $__tool_directory__/join_nucmer.pl $output_file ${" ".join(map(str, $input_file))}
+  ]]>
+  </command>
+
+  <inputs>
+    <param name="input_file" format="tsv" type="data" multiple="true" label="show-snps tabular output" help="join mutiple nucmer output files" />
+  </inputs>
+
+  <outputs>
+    <data format="tsv" name="output_file" label="${tool.name} on ${on_string} consolidated variants file" />
+  </outputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  <help>
+	**What it does?**
+
+	This tool is used to merge variant calls, in nucmer format, into a single tabular file. The output file will have as may columns as
+	the number of genomes provided in input. And as many rows as the number of variants observed in the genomes. For every genome assembly and
+	variant a simple binary code 1= present, 0=absent will be used to indicate whether that genome carries a specific variant.
+	This table should be provided to the FunAnn tool to obtain the functional annotation of the variants.
+	
+  </help>
+
+  <tests>
+    <test>
+    </test>
+  </tests>
+
+</tool>