<?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>