<tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@">
    <description>construct a dynamic succinct variation graph</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$infile' ./infile.${infile.ext} &&

vg deconstruct
#if $path:
    --path '${','.join([$p for $p in $path])}'
#end if
#if $path_prefix
    --path-prefix '${','.join([$p for $p in $path_prefix])}'
#end if
#if $alt_prefix
    --alt-prefix '${','.join([$p for $p in $alt_prefix])}'
#end if
#if $snarls:
    --snarls '$snarls'
#end if
$path_traversals  ## -e
--threads=\${GALAXY_SLOTS:-1}
./infile.${infile.ext}

> '$output'

    ]]></command>
    <inputs>
        <param name="infile" type="data" format="xg,odgi" label="Graph files" />
        <param argument="--path" type="text" value="" label="A reference path to deconstruct against"
            help="comma-separated list accepted">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference"
            help="comma-separated list accepted">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF"
            help="comma-separated list accepted">
            <sanitizer>
                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true"
            help="from `vg snarls` to avoid recomputing" />

        <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false"
            label="Only consider traversals that correspond to paths in the grpah" />
    </inputs>
    <outputs>
        <data name="output" format="vcf" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="hla.xg" />
            <param name="path" value="gi|568815592:29791752-29792749" />
            <param name="path_traversals" value="true" />
            <output name="output" file="hla_variants.vcf" />
        </test>
    </tests>
    <help><![CDATA[
variation graph (vg) deconstruct module
-----------------------------------

Creates VCF records for Snarls present in a graph (relative to a chosen reference path).

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