<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
  <description>SNP/indel variant calling from VCF/BCF</description>
  <macros>
    <token name="@EXECUTABLE@">call</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command detect_errors="aggressive"><![CDATA[
bcftools @EXECUTABLE@

## Consensus/variant calling section
#if $sec_consensus_variant_calling.select_caller == "consensus":
    --consensus-caller
#else:
    --multiallelic-caller
#end if

#if $sec_consensus_variant_calling.constraints.constrain_select == "alleles":
  --constrain alleles
#elif $sec_consensus_variant_calling.constraints.constrain_select == "trio":
  --constrain trio
  --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del}
  --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}"
#end if

#if $sec_consensus_variant_calling.prior:
  --prior "${sec_consensus_variant_calling.prior}"
#end if
${sec_consensus_variant_calling.chromosome_X}
${sec_consensus_variant_calling.chromosome_Y}


## File format section
#if str($sec_default.select_output_type) != "__none__":
  --output-type "${sec_default.select_output_type}"
#end if
@SEC_DEF_REGIONS@
@SEC_DEF_SAMPLES@
@SEC_DEF_TARGETS@


## Input/output section
${sec_input_output.keep_alts}
#set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat])
#if $values_sec_input_output_format_fields:
  --format-fields "${values_sec_input_output_format_fields}"
#end if

#if str($sec_input_output.gvcf) != "":
  --gvcf "${sec_input_output.gvcf}"
#end if

${sec_input_output.insert_missed}
${sec_input_output.keep_masked_ref}

#if str($sec_input_output.skip_variants) != "__none__":
  --skip-variants "${sec_input_output.skip_variants}"
#end if

${sec_input_output.variants_only}

## Primary Input/Outputs

$input_file
>
$output_file
]]>
</command>
  <inputs>
    <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" />
    <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
      <param name="select_caller" label="Calling Method" type="select">
        <option value="consensus">the original calling method (-c, --consensus-caller)</option>
        <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option>
      </param>
      <conditional name="constraints" label="Constraints">
        <param name="constrain_select" label="Constraints" type="select" argument="-C">
          <option value="__none__" selected="True">No constraints</option>
          <option value="alleles">call genotypes given alleles (alleles)</option>
          <option value="trio">call genotypes given the father-mother-child constraint (trio)</option>
        </param>
        <when value="__none__" />
        <when value="alleles" />
        <when value="trio">
          <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/>
          <param name="novel_ins" label="Novel Rate: Insertions" type="float" default="1e-9" optional="True" help="mutation rate of insertions according to their length" argument="--novel-rate" />
          <param name="novel_del" label="Novel Rate: Deletions" type="float" default="1e-9" optional="True" help="mutation rate of deletions according to their length" argument="--novel-rate" />
          <param name="pval_threshold" label="Pval Threshold" type="float" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" argument="--pval-treshold"/>
        </when>
      </conditional>
      <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" />
      <param name="chromosome_X" label="Chromosome X" type="boolean" truevalue="--chromosome-X" falsevalue="" help="haploid output for male samples (requires PED file with -s)" argument="--chromosome-X"/>
      <param name="chromosome_Y" label="Chromosome Y" type="boolean" truevalue="--chromosome-Y" falsevalue="" help="haploid output for males and skips females (requires PED file with -s)" argument="--chromosome-Y"/>
    </section>
    <section name="sec_default" expanded="true" title="Default Options">
      <expand macro="macro_select_output_type" />
      <expand macro="macro_regions" />
      <expand macro="macro_samples" />
      <expand macro="macro_targets" />
    </section>
    <section name="sec_input_output" expanded="true" title="Input/output Options">
      <param name="keep_alts" label="Keep Alts" type="boolean" truevalue="--keep-alts" falsevalue="" help="keep all possible alternate alleles at variant sites" argument="--keep-alts"/>
      <repeat name="format_fields_repeat" title="Format Fields">
        <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" />
      </repeat>
      <param name="gvcf" label="Gvcf" type="integer" optional="True" help="output gVCF blocks of homozygous REF calls. The parameter is the minimum per-sample depth required to include a site in the non-variant block." argument="--gvcf"/>
      <param name="insert_missed" label="Insert Missed" type="boolean" truevalue="--insert-missed" falsevalue="" help="output also sites missed by mpileup but present in -T" argument="--insert-missed"/>
      <param name="keep_masked_ref" label="Keep Masked Ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" help="keep sites with masked reference allele (REF=N)" argument="--keep-masked-ref"/>
      <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants">
        <option value="__none__" selected="True">Don't skip any</option>
        <option value="indels">Skip indels</option>
        <option value="snps">Skip snps</option>
      </param>
      <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/>
    </section>
  </inputs>
  <outputs>
    <data name="output_file" format="vcf">
      <change_format>
        <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" />
        <when input="sec_file_format|select_output_type" value="u" format="bcf" />
        <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" />
        <when input="sec_file_format|select_output_type" value="v" format="vcf" />
      </change_format>
    </data>
  </outputs>
  <tests>
      <test>
          <param name="input_file" value="mpileup.vcf" />
          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
          <param name="sec_input_output|variants_only" value="--variants-only" />
          <param name="sec_file_format|select_output_type" value="v" />
          <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" />
      </test>
      <test>
          <param name="input_file" value="mpileup.vcf" />
          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
          <param name="sec_input_output|variants_only" value="--variants-only" />
          <param name="sec_input_output|gvcf" value="0" />
          <param name="sec_file_format|select_output_type" value="v" />
          <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" />
      </test>
  </tests>
  <help>
      <![CDATA[
      **bcftools call**

      SNP/indel variant calling from VCF/BCF. To be used in conjunction with
      samtools mpileup. This command replaces the former "bcftools view"
      caller. Some of the original functionality has been temporarily lost in
      the process of transition to htslib, but will be added back on popular
      demand. The original calling model can be invoked with the -c
      option.
      ]]>
  </help>
  <expand macro="citations" />
</tool>