<?xml version="1.0"?>
<tool id="poretools_stats" name="Read length statistics" version="@VERSION@.0">
    <description>from a set of FAST5 files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
        poretools stats --type $type $detailed '$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="detailed" argument="--full-tsv" type="boolean" truevalue="--full-tsv" falsevalue="" label="Output detailed statistics" />
        <expand macro="stat_options" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" />
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="type" value="fwd" />
            <param name="detailed" value="true" />
            <output name="output" file="poretools-stats-out1.tabular" ftype="tabular" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="type" value="rev" />
            <param name="detailed" value="false" />
            <output name="output" file="poretools-stats-out2.tabular" ftype="tabular" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="type" value="2D" />
            <param name="detailed" value="true" />
            <output name="output" file="poretools-stats-out3.tabular" ftype="tabular" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="type" value="best" />
            <param name="detailed" value="false" />
            <output name="output" file="poretools-stats-out4.tabular" ftype="tabular" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="type" value="all" />
            <param name="detailed" value="true" />
            <output name="output" file="poretools-stats-out5.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
        Collect read size statistics from a set of FAST5 files.
    </help>
    <expand macro="citations" />
</tool>