<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
    <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>
    <macros>
        <token name="@EXECUTABLE@">norm</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_ref
@PREPARE_FASTA_REF@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@

bcftools @EXECUTABLE@

#set $section = $sec_ref
@FASTA_REF@
${section.do_not_normalize}
#if $section.check_ref:
  --check-ref "${section.check_ref}"
#end if

## Default section
#set $section = $sec_default
#if $section.rm_dup:
  --rm-dup "${section.rm_dup}"
#end if
#if $section.multiallelics:
  #set $mtype = ''
  #if $section.multiallelic_types:
    #set $mtype = $section.multiallelic_types
  #end if
  --multiallelics "${section.multiallelics}${mtype}" 
#end if
${section.strict_filter}
#if $section.site_win:
  --site-win "${section.site_win}"
#end if

#set $section = $sec_restrict
@REGIONS@
@TARGETS@

@OUTPUT_TYPE@
@THREADS@

## Primary Input/Outputs
@INPUT_FILE@
> "$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" />
        </section>
        <section name="sec_ref" expanded="false" title="Reference Options">
            <expand macro="macro_fasta_ref" />
            <param name="check_ref" type="select" label="Check REF" optional="true" 
                    help="What to do when incorrect or missing REF allele is encountered">
                <option value="e">check REF alleles and exit (e)</option>
                <option value="w">warn (w)</option>
                <option value="x">exclude (x)</option>
                <option value="s">set bad sites (s)</option>
                <option value="wx">warn and exclude (wx)</option>
                <option value="ws">warn and set bad sites (ws)</option>
            </param>
            <param name="do_not_normalize" type="boolean" truevalue="--do-not-normalize" falsevalue="" label="Skip Normalization, just set REF allele" 
                   help="Do not normalize indels, just fix or set the REF allele from the reference (-N, --do-not-normalize with -m or -c s)" />
        </section>

        <section name="sec_default" expanded="false" title="Default Options">
            <param name="rm_dup" type="select" label="Rm Dup" optional="true" 
                   help="Remove duplicate snps|indels|both|any">
                <option value="snps">snps</option>
                <option value="indels">indels</option>
                <option value="both">both</option>
                <option value="any">any</option>
            </param>
            <param name="multiallelics" type="select" label="~multiallelics" optional="true">
                <option value="-">split multiallelic sites into biallelic records (-)</option> 
                <option value="+">join biallelic sites into multiallelic records (+)</option> 
            </param>
            <param name="multiallelic_types" type="select" label="variant types which should be split or merged" optional="true">
                <option value="snps">snps - only SNP records should be split or merged</option>
                <option value="indels">indels - only indel records should be split or merged</option>
                <option value="both">both - records should be split or merged</option>
                <option value="any">any - SNPs and indels should be merged into a single record</option>
            </param>
            <param name="strict_filter" type="boolean" truevalue="--strict-filter" falsevalue="" label="Strict Filter" 
                   help="When merging (-m+), merged site is PASS only if all sites being merged PASS" />
            <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" 
                   help="(-w, --site-win) Buffer for sorting lines which changed position during realignment" />
        </section>

        <expand macro="macro_select_output_type" />
    </inputs>
    <outputs>
        <expand macro="macro_vcf_output"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="norm.vcf" />
            <param name="fasta_ref" ftype="fasta" value="norm.fa" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="T,TAACCCTA" />
                    <not_has_text text="TAA,TAACCCTAAA" />
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input_file" ftype="vcf" value="norm.split.vcf" />
            <param name="multiallelics" value="-" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <not_has_text text="TAA,TAACCCTAAA" />
                    <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAA\t"/>
                    <has_text_matching expression="1\t105\t.\tTAAACCCTAAA\tTAACCCTAAA\t"/>
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input_file" ftype="vcf" value="norm.split.vcf" />
            <param name="fasta_ref" ftype="fasta" value="norm.fa" />
            <param name="multiallelics" value="-" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <not_has_text text="TAA,TAACCCTAAA" />
                    <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
                    <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
            <param name="multiallelics" value="+" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="TAA,TAACCCTAAA" />
                    <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tFAIL"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="norm.merge.vcf" />
            <param name="multiallelics" value="+" />
            <param name="strict_filter" value="true" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="TAA,TAACCCTAAA" />
                    <has_text_matching expression="2\t114\t.\tTC\tTTCC,TTC\t999\tPASS"/>
                </assert_contents>
            </output>
        </test>

        <test>
            <param name="input_file" ftype="vcf" value="norm.setref.vcf" />
            <param name="fasta_ref" ftype="fasta" value="norm.fa" />
            <param name="do_not_normalize" value="true" />
            <param name="check_ref" value="s" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
                    <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
                </assert_contents>
            </output>
        </test>

    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================


Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows.

@REGIONS_HELP@
@TARGETS_HELP@

@BCFTOOLS_MANPAGE@#@EXECUTABLE@

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