--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam2msa.xml	Wed May 16 17:34:58 2018 -0400
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool id="bioext_bam2msa" name="Convert BAM" version="@VERSION@.0">
+  <description>to FASTA multiple sequence alignment</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code"><![CDATA[
+    bam2msa
+        #if $region_start and $region_end:
+            -r $region_start:$region_end
+        #end if
+        '$input' '$output'
+    ]]></command>
+  <inputs>
+    <param name="input" type="data" format="bam,sam" label="Input BAM file"/>
+    <param name="region_start" type="integer" value="0" optional="True" label="Starting coordinate" help="Leave blank to extract all sequences"/>
+    <param name="region_end" type="integer" value="0" optional="True" label="End coordinate"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out1.bam"/>
+      <output name="output" file="bam2msa-out1.fa"/>
+    </test>
+    <test>
+      <param name="input" ftype="bam" value="bealign-out2.bam"/>
+      <output name="output" file="bam2msa-out2.fa"/>
+    </test>
+  </tests>
+  <help>Extract MSA from a BAM file</help>
+  <expand macro="citations"/>
+</tool>