<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@">
    <description>plugin Sets genotypes</description>
    <macros>
        <token name="@EXECUTABLE@">setGT</token>
        <token name="@PLUGIN_ID@">setgt</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 = $sec_plugin
--
-t '$section.target_gt'
--new-gt '$section.new_gt'
> '$output_file'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <section name="sec_plugin" expanded="true" title="Plugin Options">
            <param name="target_gt" type="select" label="Target genotypes to change">
                <option value="./.">./. completely missing (. or ./., depending on ploidy)</option>
                <option value="./x">./x partially missing (./0 or .|1)</option>
                <option value=".">. partially or completely missing</option>
                <option value="a">a all genotypes</option>
            </param>
            <param name="new_gt" type="select" label="New genotypes to set">
                <option value=".">. missing (. or ./., keeps ploidy)</option>
                <option value="0">0 reference allele</option>
                <option value="M">M major allele</option>
                <option value="p">p phased genotype</option>
                <option value="u">u unphase genotype and sort by allele (1|0 becomes 0/1)</option>
            </param>
	</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="target_gt" value="." />
            <param name="new_gt" value="0" />
            <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>