<?xml version="1.0"?>
<tool id="get_hrun" name="Get homopolymer run length" version="@VERSION@+galaxy0" profile="@PROFILE@" license="MIT">
    <description>Annotate indel variants with homopolymer context</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        ln -s '${reference}' ref.fa &&
        samtools faidx ref.fa &&
        python '${__tool_directory__}/get_hrun.py' --reference ref.fa --in-vcf '${in_vcf}' --out-vcf '${out_vcf}'
]]></command>
    <inputs>
        <param argument="--in-vcf" type="data" format="vcf" label="Input VCF"/>
        <param argument="--reference" type="data" format="fasta" label="Input Reference FASTA"/>
    </inputs>
    <outputs>
        <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="in_vcf" value="in.vcf"/>
            <param name="reference" value="reference.fasta"/>
            <output name="out_vcf" value="out.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

@WID@

**Inputs**
- VCF file
- Reference file for that VCF
**Outputs**
- VCF with annotated homopolymers
]]></help>
    <expand macro="citations"/>
</tool>