<?xml version="1.0"?>
<tool id="seqtk_telo" name="seqtk_telo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description>find telomeres</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk telo
-m '$m'
-p '$p'
-d '$d'
-s '$s'
$P
'$in_file'
> '$default'
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
        <param argument="-m" type="text" value="CCCTAA" label="Telomere repeat to search for. Default is vertebrate" />
        <param argument="-p" type="integer" value="1" label="Penalty for a non-repeat" />
        <param argument="-d" type="integer" value="2000" label="Maximum drop" />
        <param argument="-s" type="integer" value="300" label="Minimum score" />
        <param argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="Print scoring" />
    </inputs>
    <outputs>
        <data name="default" format="bed" label="${tool.name} on ${on_string}: telomers"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_telo.fa"/>
            <output name="default" file="seqtk_telo.out" ftype="bed"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_telo.fa.gz" ftype="fasta.gz"/>
            <output name="default" file="seqtk_telogz.out" ftype="bed"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Identifies telomeres using a default vertebrate repeat sequence CCCTAA, or a user supplied one


::

     Usage: seqtk telo [options] <in.fq>
     Options:
     -m STR     motif [CCCTAA]
     -p INT     penalty [1]
     -d INT     max drop [2000]
     -s INT     min score [300]
     -P         print scoring


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