<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@">
    <description>plugin Determine sample sex by checking genotypes in haploid regions</description>
    <macros>
        <token name="@EXECUTABLE@">vcf2sex</token>
        <token name="@PLUGIN_ID@">vcf2sex</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@

## Primary Input/Outputs
@INPUT_FILE@
## Plugin section
--
#set $section = $sec_plugin
#if $section.background:
  --background "${section.background}"
#end if
#if $section.guess:
  --guess $section.guess
#end if
#if $section.min_hets:
  --min-hets $section.min_hets
#end if
#if $section.nsites:
  --nsites $section.nsites
#end if
@PLOIDY_FILE@
${section.verbose}
| tee "$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="background" type="text" value="" optional="true" label="background region">
                <help>
                   Diploid region to determine normal hom/hets counts [X:60001-2699520]
                </help>
                <validator type="regex" message="">^(\w+:\d+-\d+)?$</validator>
            </param>
            <param name="guess" type="select" label="guess - determine ploidy by tag"  optional="true"
                   help="Determine ploidy by counting hom/hets (GT) or most likely genotypes (PL or GL)">
                  <option value="GT">counting hom/hets (GT)</option> 
                  <option value="GL">most likely genotypes (GL)</option> 
                  <option value="PL">most likely genotypes (PL)</option> 
              </param>
  
              <param name="min_hets" type="float" value=".3" min="0." max="1." optional="true" label="min-hets - minimum fraction of hets in diploid regions [0.3]" 
                     help="(\-\-min-hets)"/>
              <param name="nsites" type="integer" value="10" min="0" optional="true" label="nsites - number of sites to check per region"
                     help="(ignored with --guess) [10]"/>
      
              <expand macro="macro_ploidy_file" />
              <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Verbose" 
                     help="Print debugging information on plugin failure" />

        </section>
    </inputs>
    <outputs>
        <data name="output_file" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
            <param name="nsites" value="5" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="MALE"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
            <param name="guess" value="GT" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="MALE"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="vcf2sex.vcf" />
            <param name="guess" value="GT" />
            <param name="nsites" value="5" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="MALE"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@ plugin
=====================================

@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

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