<?xml version="1.0"?>
<tool id="poretools_events" name="Extract nanopore events" version="@VERSION@.1">
    <description>from a set of sequencing reads</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
        poretools events $precalled '$input' > '$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="precalled" argument="--pre-basecalled" type="boolean" truevalue="--pre-basecalled" falsevalue="" label="Report pre-basecalled events" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="precalled" value="false" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="2901"/>
                    <has_text text="template"/>
                    <has_text text="complement"/>
                    <not_has_text text="pre_basecalled"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <expand macro="test_input" />
            <param name="precalled" value="true" />
            <output name="output" ftype="tabular">
                <assert_contents>
                    <has_n_lines n="3083"/>
                    <not_has_text text="template"/>
                    <not_has_text text="complement"/>
                    <has_text text="pre_basecalled"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        Extract the raw nanopore events from each FAST5 file.
    </help>
    <expand macro="citations" />
</tool>