<?xml version="1.0"?>
<tool id="seqtk_listhet" name="seqtk_listhet" version="@TOOL_VERSION@.1">
    <description>extract the position of each het</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk listhet
'$in_file'  | awk 'BEGIN{print "#chr\tposition\tbase"}1'
> '$default'
]]></command>
    <inputs>
        <expand macro="in_faq"/>
    </inputs>
    <outputs>
        <data name="default" format="tabular" label="Positions of heterozygous bases in $in_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_listhet.fa"/>
            <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_listhet.fa.gz" ftype="fasta.gz"/>
            <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Lists regions of heterozygosity.

::

    >ambig
    ACGTMRWSYKVHDBN

The seqtk suite recognises MRWSYK:

::

    #chr    position  base
    ambig   5         M
    ambig   6         R
    ambig   7         W
    ambig   8         S
    ambig   9         Y
    ambig   10        K


@ATTRIBUTION@
    ]]></help>
    <expand macro="citation" />
</tool>