<?xml version="1.0"?>
<tool id="bioext_bam2msa" name="Convert BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>to FASTA multiple sequence alignment</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ## avoid bam2msa to create .bai in inputdir
        ln -sf '$input' input_bam &&
        ln -sf '$input.metadata.bam_index' input_bam.bai &&
        bam2msa
            #if $region_start and $region_end:
                -r $region_start:$region_end
            #end if
            'input_bam'
            '$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="bam2msa-in1.bam"/>
            <output name="output" file="bam2msa-out1.fa"/>
        </test>
        <test>
            <param name="input" ftype="bam" value="bam2msa-in2.bam"/>
            <output name="output" file="bam2msa-out2.fa"/>
        </test>
    </tests>
    <help>Extract MSA from a BAM file</help>
    <expand macro="citations"/>
</tool>