interactivetool_panoply.xml

<tool id="interactive_tool_panoply" tool_type="interactive" name="Panoply" version="@VERSION@">
    <description>interative plotting tool for geo-referenced data</description>
    <macros>
    <token name="@VERSION@">4.5.1</token>
    </macros>
    <requirements>
        <container type="docker">quay.io/nordicesmhub/docker-panoply:@VERSION@</container>
    </requirements>
    <entry_points>
        <entry_point name="Panoply on $infile.display_name" requires_domain="True">
            <port>5800</port>
        </entry_point>
    </entry_points>
    <command detect_errors="exit_code">
    <![CDATA[
    mkdir output &&
        mkdir /config/home  &&
        mkdir /config/home/output &&
        export HOME=/config/home &&
        cp '$infile' '/config/home/$infile.display_name' &&
        mkdir /config/home/.gissjava &&
        cd /config/home/.gissjava    &&
        tar xvf /opt/PanoplyJ/colorbars.tar &&
        cd - &&
        /init ;
        echo "Galaxy Panoply version @VERSION@" > output/version.txt &&
        cp /config/home/output/* output/ | true &&
        cd output &&
        sleep 2 &&
        for file in *; do mv "\$file" "\${file// /_}"; done &&
        for file in *; do mv "\$file" "\$file.\${file\#\#*.}"; done
    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="netcdf,h5" label="netcdf"/>
    </inputs>
    <outputs>
        <collection name="outputs" type="list" label="Panoply outputs">
            <discover_datasets pattern="__name_and_ext__" directory="output" />
        </collection>
    </outputs>
    <tests>
    </tests>
    <help><![CDATA[
        `Panoply <https://www.giss.nasa.gov/tools/panoply/>`_ plots geo-referenced and other arrays from netCDF, HDF, GRIB, and other datasets.
    ]]>
    </help>
</tool>