<?xml version="1.0"?>
<tool id="seqtk_hety" name="seqtk_hety" version="@TOOL_VERSION@.1">
    <description>regional heterozygosity</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk hety
-w $w
-t $t
$m
'$in_file' | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
> '$default'
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
        <param argument="-w" type="integer" value="50000" label="Window size" />
        <param argument="-t" type="integer" value="5" label="# start positions in a window" />
        <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Treat lowercases as masked" />
    </inputs>
    <outputs>
        <data name="default" format="tabular" label="Heterozygous regions in $in_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_hety.fa"/>
            <param name="w" value="8"/>
            <output name="default" file="seqtk_hety.out" ftype="tabular"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_hety.fa.gz" ftype="fasta.gz"/>
            <param name="w" value="8"/>
            <output name="default" file="seqtk_hety.out" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Reports on heterozygosity over a region

::

    >het_region
    ACTTTACATCGAGCMMMMMMMACAGTACTG

As can be seen in the following output:

::

    #chr        start  end  A       B   num_het
    het_region  0      8    0.00    8   0
    het_region  8      9    0.00    8   0
    het_region  9      10   0.00    8   0
    het_region  10     11   0.00    8   0
    het_region  11     12   0.00    8   0
    het_region  12     13   0.00    8   0
    het_region  13     14   0.00    8   0
    het_region  14     15   1.00    8   1
    het_region  15     16   2.00    8   2
    het_region  16     17   3.00    8   3
    het_region  17     18   4.00    8   4
    het_region  18     19   5.00    8   5
    het_region  19     20   6.00    8   6
    het_region  20     21   7.00    8   7
    het_region  21     22   7.00    8   7
    het_region  22     23   6.00    8   6
    het_region  23     24   5.00    8   5
    het_region  24     25   4.00    8   4
    het_region  25     26   3.00    8   3
    het_region  26     27   2.00    8   2
    het_region  27     28   1.00    8   1
    het_region  28     29   0.00    8   0
    het_region  29     30   0.00    1   0

If you know what A and B are measures of, please `submit an issue <https://github.com/galaxyproject/tools-iuc/issues>`__ and it will be corrected

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