<?xml version="1.0"?>
<tool id="poretools_hist" name="Generate histogram" version="@VERSION@.0">
    <description>of nanopore read lengths</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
        poretools hist '$input' --saveas histogram.$extension --min-length $min_length
            --max-length $max_length --num-bins $num_bins $theme_bw && mv histogram.$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" />
        <expand macro="plot_options" />
        <expand macro="length_options" />
        <param name="num_bins" argument="--num-bins" type="integer" value="50" label="Number of bins in the histogram" />
    </inputs>
    <outputs>
        <expand macro="image_output" />
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="png" />
            <output name="output" file="poretools-hist-out1.png" ftype="png" lines_diff="73" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="pdf" />
            <output name="output" file="poretools-hist-out1.pdf" ftype="pdf" lines_diff="36" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="svg" />
            <output name="output" file="poretools-hist-out1.svg" ftype="svg" lines_diff="138" />
        </test>
    </tests>
    <help>
        Draw a histogram of read lengths in one or more nanopore reads.
    </help>
    <expand macro="citations" />
</tool>