<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
    <description>plugin  Fix ploidy</description>
    <macros>
        <token name="@EXECUTABLE@">fixploidy</token>
        <token name="@PLUGIN_ID@">fixploidy</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@

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
--
@PLOIDY_FILE@
#if $section.sex:
--sex "${section.sex}"
#end if
## Only default tag GT is currently accepted  
--tags "$section.tags"  
> "$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">
            <expand macro="macro_ploidy_file" />
            <param name="sex" type="data" format="tabular" label="Sample Sex file" optional="true"/>
            <param name="tags" type="hidden" value="GT" label="tags"/>
        </section>
        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="fixploidy.vcf" />
            <param name="sex" ftype="tabular" value="fixploidy.samples" />
            <param name="ploidy_file" ftype="tabular" value="fixploidy.ploidy" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="3000004\txx\tC\tCTTTT\t11\tq11\tFLAG;IINT=11;IFLT=1.1;ISTR=xxx\tGT:FINT:FFLT:FSTR\t0/0/0/0/0/0:11:1.1:x\t0/0/0/0/0/0/0:11:1.1:xxx\t0|0|0|0|0|0|0|0:11:1.1:xxx" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

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