collate.xml

<tool id="alevin_fry_collate" name="Alevin-Fry Collate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
    <description>Collate a RAD file by corrected cell barcode</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir input1 &&
        ln -s '$input1' input1 &&
        mkdir input2 &&
        ln -s '$input2' input2 &&
        alevin-fry collate --input-dir input1 --rad-dir input2
    ]]></command>
    <inputs>
        <param type="data" name="input1" label="Output of 'Alevin-Fry Generate Permit List'" format="directory"/>
        <param type="data" name="input2" label="RAD file to be collated" format="rad"/>
    </inputs>
    <outputs>
        <param type="data" name="output1" label="${tool.name} on ${on_string}: $input2.collated" format="rad"/>
        <param type="data" name="output2" label="${tool.name} on ${on_string}: collate" format="json"/>
    </outputs>
    <tests>
        <test>
            <!-- add tests -->
        </test>
    </tests>
    help
    <help>
        help
    </help>
    <expand macro="citations"/>
</tool>