<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>plugin Sets genotypes</description>
    <macros>
        <token name="@EXECUTABLE@">setGT</token>
        <token name="@PLUGIN_ID@">setgt</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />
    <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
@REGIONS@
@TARGETS@

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILE@

## Plugin section
#set $section = $sec_plugin
--
--target-gt '$section.target_gt'
--new-gt '$section.new_gt'

#set $section = $sec_restrict
@INCLUDE@
@EXCLUDE@
> '$output_file'
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" 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="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>
                <option value="b">b heterozygous genotypes failing two-tailed binomial test</option>
                <option value="q">q select genotypes using -i/-e options</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 (e.g. 0/0 or 0, keeps ploidy)</option>
                <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option>
                <option value="M">M major allele</option>
                <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</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>
        <test>
            <param name="input_file" ftype="vcf" value="plugin1.vcf" />
            <section name="sec_restrict">
                <param name="exclude" value="FMT/GQ>20"/>
            </section>
            <section name="sec_plugin">
                <param name="target_gt" value="q" />
                <param name="new_gt" value="." />
            </section>
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="DP4=1,2,3,4;INDEL;STR=test" />
                    <has_n_lines n="38"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

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