--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clonalframeML.xml	Fri Mar 05 14:32:29 2021 +0000
@@ -0,0 +1,35 @@
+<tool id="clonalframeMLtool" name="clonalframeML" version="1.0">
+  <description>a software package that performs efficient inference of recombination in bacterial genomes</description>
+<requirements>
+  <requirement type="package" version="1.12">clonalframeml</requirement>
+</requirements>
+
+  <command>'conda activate' ClonalFrameML $input $output </command>
+  <inputs>
+	  <param format="nwk" name="input" type="data" label="Genome fasta file : " multiple="false" display="checkboxes"/>
+	  <param format="fasta" name="input1" type="data" label="Genome fasta file : " multiple="false" display="checkboxes"/>
+
+ </inputs>
+
+ <outputs>
+    <data format="txt" name="output" />
+ </outputs>
+
+ <tests>
+    <test>
+            <param name="input" value="tree_45ind_190kSNP.withST.nwk" />
+            <param name="input" value="190ksnp_alignment_KP2.fa" />
+        <output name="output" file="results.txt" />
+    </test>
+</tests>
+
+  <help>
+For full documentation, please go to the ClonalframeML wiki (https://github.com/katholt/Kleborate/wiki)
+  </help>
+  <citations>
+         <citation type="doi">10.1371/journal.pcbi.1004041</citation>
+                </citations>
+</tool>
+
+
+