<?xml version="1.0"?>
<tool id="poretools_occupancy" name="Plot performance" version="@VERSION@.1">
    <description>per cell in nanopore reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
@MPLBACKEND@
poretools occupancy
    '$input'
    --saveas occupancy.$extension
    --plot-type $plot_type
&&
mv occupancy.$extension '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
        <param name="extension" type="select" label="File format for histogram">
            <option value="png">PNG</option>
            <option value="pdf">PDF</option>
            <option value="svg">SVG</option>
        </param>
        <param name="plot_type" argument="--plot-type" type="select" label="Plot type to generate">
            <option value="read_count">Read count</option>
            <option value="total_bp">Total base pairs</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="image_output" />
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="png" />
            <param name="plot_type" value="read_count" />
            <output name="output" file="poretools-occupancy-out1.png" ftype="png" compare="sim_size" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="pdf" />
            <param name="plot_type" value="total_bp" />
            <output name="output" file="poretools-occupancy-out1.pdf" ftype="pdf" lines_diff="384" />
        </test>
    </tests>
    <help>
        Plot the throughput performance of each pore on the flowcell during a given sequencing run.
    </help>
    <expand macro="citations" />
</tool>