<?xml version="1.0"?>
<tool id="poretools_squiggle" name="Plot signals" version="@VERSION@.0">
    <description>for nanopore reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
        poretools squiggle '$input' --saveas $extension --num-facets $num_facets
            $theme_bw
    ]]>
    </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" />
        <param name="num_facets" argument="--num-facets" type="integer" value="6" label="Number of plot facets" />
    </inputs>
    <outputs>
        <data format="txt" name="output">
            <discover_datasets pattern="__designation_and_ext__" directory="." visible="true" />
        </data>
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="png" />
            <output name="output">
                <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.png" lines_diff="986" />
                <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.png" lines_diff="883" />
            </output>
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="pdf" />
            <output name="output">
                <discovered_dataset designation="2016_3_4_3507_1_ch128_read430_strand.fast5" file="poretools-squiggle-out1-1.pdf" lines_diff="35" />
                <discovered_dataset designation="2016_3_4_3507_1_ch128_read95_strand.fast5" file="poretools-squiggle-out1-2.pdf" lines_diff="35" />
            </output>
        </test>
    </tests>
    <help>
        Plot the observed signals for FAST5 reads.
    </help>
    <expand macro="citations" />
</tool>