<tool id="dr_disco_bam_extract" name="Dr. Disco (bam-extract)" version="@TOOL_VERSION@">
    <description>Extracts reads from two targeted regions</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements" />
    <expand macro="version_command"/>
    
    <command detect_errors="exit_code"><![CDATA[
        dr-disco bam-extract
            '$region1'
            '$region2'
            '$input_alignment'
            '$output'
    ]]></command>

    <inputs>
        <param name="input_alignment" type="data" format="bam" label="Discordant alignment file of STAR)" />
        <param name="region1" type="text" value="chr21:39737183-40035618" label="Genomic region 1" />
        <param name="region2" type="text" value="chr21:42834478-42882085" label="Genomic region 2" />
    </inputs>

    <outputs>
        <data name="output" format="bam" label="${tool.name} on ${input_alignment.name}" />
    </outputs>
    
    <tests>
        <test>
            <param name="input_alignment" value="bam_extract.bam" />
            <param name="region1" value="chr21:39737183-40035618" />
            <param name="region2" value="chr21:42834478-42882085" />
            
            <output name="output" file="bam_extract.bam" />
        </test>
        <test>
            <param name="input_alignment" value="bam_extract.bam" />
            <param name="region1" value="chr22:39737183-40035618" />
            <param name="region2" value="chr11:42834478-42882085" />
            
            <output name="output" file="bam_extract.empty.bam" />
        </test>
    </tests>
    
    <help><![CDATA[

**What it does**

Extract reads that have their mate within one of two chromosomal positions (and also takes mates that correspond to these reads)

Regions are in the format:
   chr1:123-546
    ]]></help>
    
     <expand macro="citations"/>
</tool>