view coverm.xml @ 2:76061f7c682c draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/coverm commit 98ef2779cb5f4784409ceb468a2250da518c53c4-dirty"

<tool id="coverm" name="coverm" version="@VERSION@">
    <description>Read coverage calculator for metagenomics</description>
    <macros>
        <token name="@VERSION@">0.3.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">coverm</requirement>
    </requirements>
    <version_command>coverm --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        coverm contig
        -t \${GALAXY_SLOTS}
        --methods metabat
        --bam-files $bam 
        > depth.tsv
    ]]></command>
    
    <inputs>
        <param name="bam" type="data" format="bam" label="Input bam file" />
    </inputs>

    <outputs>
        <data name="depth" format="json" label="${tool.name} on ${on_string} Depth" from_work_dir="depth.tsv"/>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[

    Documentation can be found at `<https://github.com/wwood/CoverM>`_.

    ]]></help>
</tool>