<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
    <description>plugin Set missing genotypes</description>
    <expand macro="bio_tools" />
    <macros>
        <token name="@EXECUTABLE@">missing2ref</token>
        <token name="@PLUGIN_ID@">missing2ref</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@

bcftools plugin @EXECUTABLE@

## VCF input section
#set $section = $sec_restrict
@INCLUDE@
@EXCLUDE@
@REGIONS@
@TARGETS@

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILE@

## Plugin section
#set $section = $sec_plugin
#if $section.phased or $section.major:
--
${section.phased}
${section.major}
#end if
> '$output_file'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <section name="sec_plugin" expanded="true" title="Plugin Options">
            <param name="phased" type="boolean" truevalue="--phased" falsevalue="" checked="false" label="Phased" help="Set to 0|0" />
            <param name="major" type="boolean" truevalue="--major" falsevalue="" checked="false" label="Major" help="Set to major allele" />
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="0/0:245" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

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