<?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>