<?xml version="1.0"?>
<tool id="poretools_yield_plot" name="Collector’s curve" version="@VERSION@.1">
    <description>of sequencing yield over time</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive">
    <![CDATA[
@MPLBACKEND@
poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type
    $theme_bw
#if $skip != '0':
    --skip $skip
#end if
&& mv plot.$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="plot_type" argument="--plot-type" type="select" label="Plot reads or base pairs">
            <option value="reads">Reads</option>
            <option value="basepairs">Base pairs</option>
        </param>
        <param argument="--skip" type="integer" min="1" value="1" label="Plot only every nth point" help="Increases performance at the cost of resolution." />
        <expand macro="plot_options" />
    </inputs>
    <outputs>
        <expand macro="image_output" />
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="png" />
            <param name="plot_type" value="reads" />
            <output name="output" file="poretools-yield-plot-out1.png" ftype="png" compare="sim_size" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="svg" />
            <param name="plot_type" value="basepairs" />
            <output name="output" file="poretools-yield-plot-out2.svg" ftype="svg" lines_diff="50" />
        </test>
    </tests>
    <help>
        Create a collector’s curve reflecting the sequencing yield over time.
    </help>
    <expand macro="citations" />
</tool>