--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_convert_xmfa/xmfa2tbl.xml	Fri Jun 10 08:49:43 2022 +0000
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<tool id="xmfa2tbl" name="Convert XMFA to percent identity table" version="19.1.0.0">
+	<description></description>
+	<macros>
+		<import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+	</macros>
+	<expand macro="requirements"/>
+	<command detect_errors="aggressive"><![CDATA[
+python $__tool_directory__/xmfa2tbl.py
+$dice
+@XMFA_INPUT@
+@XMFA_FA_INPUT@
+
+> $output
+]]></command>
+	<inputs>
+		<expand macro="xmfa_input" />
+		<expand macro="xmfa_fa_input" />
+		<param type="boolean" label="use dice method in percent similarity calculation"
+			truevalue="--dice" falsevalue="" name="dice" help="The dice method alters the total similarity calculation to reflect the length of both sequences. The default for this option is true."/>
+	</inputs>
+	<outputs>
+		<data format="tabular" name="output" />
+	</outputs>
+	<tests>
+		<test>
+			<param name="xmfa" value="test.xmfa"/>
+			<param name="sequences" value="test.fa" />
+			<output name="output" file="xmfa2tbl_out.tsv"/>
+		</test>
+		<test>
+			<param name="dice" value="true"/>
+			<param name="xmfa" value="test.xmfa"/>
+			<param name="sequences" value="test.fa" />
+			<output name="output" file="xmfa2tbl_out_dice.tsv"/>
+		</test>
+	</tests>
+	<help><![CDATA[
+**What it does**
+
+This tool compares nucleotide sequences within an input XMFA file and outputs a table reflecting 
+the percent nucleotide identity between every sequence pair. Total similarity is based on 
+regions of similarity called locally collinear blocks, or LCBs. There is no penalty for gaps.
+
+**Options**
+The dice method uses the following formula to normalize considering both sequences in the pairwise comparison::
+
+	2 * number of identical matches / (query sequence length + subject sequence length)
+
+]]></help>
+		<expand macro="citations-2020" />
+</tool>