<tool id="vg_convert" name="vg convert" version="@TOOL_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$infile' ./infile.${infile.ext} &&

vg convert
$output_format
./infile.${infile.ext}
> '$output'
    ]]></command>
    <inputs>
        <param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" />
        <param name="output_format" type="select" label="Choose your output format">
            <option value="--xg-out">XG format (--xg-out)</option>
            <!--option value="- -odgi-out">odgi format (- -odgi-out)</option-->
        </param>
    </inputs>
    <outputs>
        <data name="output" format="odgi">
            <change_format>
                <when input="output_format" value="--xg-out" format="xg"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="hla.vg" ftype="vg" />
            <param name="output_format" value="--xg-out" />
            <output name="output" file="hla.xg" ftype="xg" compare="sim_size" />
        </test>
        <!--test>
            <param name="infile" value="x.vg" ftype="vg" />
            <param name="output_format" value="- -odgi-out" />
            <output name="output" file="x.odgi" ftype="odgi" compare="sim_size" />
        </test-->
    </tests>
    <help><![CDATA[

variation graph (vg) convert module
-----------------------------------

This module is converting various variant graphs into each format.

    ]]></help>
    <expand macro="citations" />
</tool>