<tool id="vg_view" name="vg view" version="@TOOL_VERSION@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
vg view
$input_format.input_format_selector
'$input_format.infile'
$output_format
--threads=\${GALAXY_SLOTS:-1}
> '$output'
    ]]></command>
    <inputs>
        <conditional name="input_format">
            <param name="input_format_selector" type="select" label="Your input is in format">
                <option value="--vg-in" selected="true">variant graph (vg)</option>
                <option value="--json-in">JSON</option>
                <option value="--gfa-in">GFA</option>
                <option value="--bam">BAM</option>
            </param>
            <when value="--vg-in">
                <param name="infile" type="data" format="vg" label="Input file in variant graph format (vg)" />
            </when>
            <when value="--gfa-in">
                <param name="infile" type="data" format="gfa1" label="Input file in Graphical Fragment Assembly (gfa)" />
            </when>
            <when value="--json-in">
                <param name="infile" type="data" format="json" label="Input file in JSON" />
            </when>
            <when value="--bam">
                <param name="infile" type="data" format="bam" label="Input file in BAM" />
            </when>
        </conditional>

        <param name="output_format" type="select" label="Choose your output format">
            <option value="--vg">VG</option>
            <option value="--json">JSON</option>
            <option value="--gfa">GFA</option>
            <option value="--dot">dot</option>
        </param>

    </inputs>
    <outputs>
        <data name="output" format="vg">
            <change_format>
                <when input="output_format" value="--dot" format="graph_dot"/>
                <when input="output_format" value="--json" format="json"/>
                <when input="output_format" value="--gfa" format="gfa1"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <conditional name="input_format">
                <param name="input_format_selector" value="--gfa-in" />
                <param name="infile" value="x.gfa" ftype="gfa1" />
            </conditional>
            <param name="output_format" value="--vg" />
            <output name="output" file="x.vg" ftype="vg" />
        </test>
        <test>
            <conditional name="input_format">
                <param name="input_format_selector" value="--vg-in" />
                <param name="infile" value="x.vg" />
            </conditional>
            <param name="output_format" value="--json" />
            <output name="output" file="x.json" ftype="json" />
        </test>
        <test>
            <conditional name="input_format">
                <param name="input_format_selector" value="--json-in" />
                <param name="infile" value="x.json" ftype="json" />
            </conditional>
            <param name="output_format" value="--vg" />
            <output name="output" file="x.vg" ftype="vg" />
        </test>
    </tests>
    <help><![CDATA[

variation graph (vg) view module
-----------------------------------

Inspect and convert variant graphs in different file formats.

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