convert.xml

<tool id="alevin_fry_convert" name="Alevin-Fry Convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
    <description>Convert BAM/SAM to RAD</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '$input' input.bam &&
        alevin-fry convert --bam input.bam --output '$output'
    ]]></command>
    <inputs>
        <param type="data" name="input" label="BAM or SAM file" format="bam,sam"/>
    </inputs>
    <outputs>
        <data name="output" label="${tool.name} on ${on_string}" format="rad"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="convert/input.bam"/>
            <output name="output" file="convert/output.rad"/>
        </test>
    </tests>
    <help><![CDATA[
        help
    ]]></help>
    <expand macro="citations"/>
</tool>