<tool id="interactive_tool_phinch" tool_type="interactive" name="Phinch Visualisation" version="0.1">
    <requirements>
        <container type="docker">shiltemann/docker-phinch-galaxy:16.04</container>
    </requirements>
    <entry_points>
        <entry_point name="Phinch Visualisation of $infile.display_name" requires_domain="True">
            <port>80</port>
        </entry_point>
    </entry_points>
    <command><![CDATA[
        ## ToDo nginx, proxy.conf etc can be removed from the container

        #import os
        #set $name = os.path.splitext(str($infile.display_name).replace(' ', '_'))[0]
        ## in case someone names the data testdata.
        rm /home/Phinch/data/testdata.biom | true &&
        ln -s '$infile' '/home/Phinch/data/${name}.biom' &&
        cd /home/Phinch/data &&
        sed -i  "s/'REPLACE_ME'/'${name}.biom'/g" /home/Phinch/scripts/readFile.js &&
        sed -i  "s/http/https/g" /home/Phinch/scripts/readFile.js &&
        ## keep it running
        cd /home/Phinch &&
        php -S 0.0.0.0:80 2>&1 > /var/log/phinch.log

    ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="biom1" label="Biom1 dataset"/>
    </inputs>
    <outputs>
        <data name="outfile" format="txt" />
    </outputs>
    <tests>
    </tests>
    <help>
        Interactive tool for visualising Biom data.
    </help>
</tool>