<?xml version='1.0' encoding='utf-8'?>
<macros>
  <token name="@VERSION@">1.2</token>
  <xml name="requirements">
    <requirements>
      <!-- This requirement handles also bcftools from BioConda channel => https://github.com/bioconda/bioconda-recipes/tree/60d2ea750430dbe0191f6f8d5639f90fc1223bd9/recipes/bcftools/1.2 -->
      <requirement type="package" version="1.2">bcftools</requirement>
    </requirements>
  </xml>
  <xml name="version_command">
      <version_command><![CDATA[bcftools 2>&1 | grep 'Version:']]></version_command>
  </xml>
  <xml name="citations">
    <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <yield />
    </citations>
  </xml>
  <xml name="macro_exclude">
    <param name="exclude" label="Exclude" help="exclude sites for which the expression is true (see man page for details)" />
  </xml>
  <xml name="macro_collapse">
      <param name="collapse" label="Collapse" type="select" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
        <option value="snps">snps</option>
        <option value="indels">indels</option>
        <option value="both">both</option>
        <option value="all">all</option>
        <option value="some">some</option>
        <option value="none" selected="True">None</option>
    </param>
  </xml>
  <xml name="macro_apply_filters_repeat">
    <repeat name="apply_filters_repeat" title="Apply Filters">
      <param name="apply_filters" label="Apply Filters" help="require at least one of the listed FILTER strings (e.g. &quot;PASS,.&quot;)" />
    </repeat>
  </xml>

  <token name="@SEC_DEF_REGIONS@">
#if $sec_default.regions_file:
  --regions-file "${sec_default.regions_file}"
#end if
  </token>
  <token name="@SEC_DEF_TARGETS@">
#if $sec_default.targets_file:
  --targets-file "${sec_default.targets_file}"
#end if
  </token>
  <token name="@SEC_DEF_SAMPLES@">
#if $sec_default.samples_file:
  --samples-file "${sec_default.samples_file}"
#end if
  </token>

  <xml name="macro_samples">
    <param name="samples_file" label="Samples File" type="data" format="data" optional="True" help="file of samples to include" />
    <param name="invert_samples_file" label="Invert Samples" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the sample file selection" />
  </xml>
  <xml name="macro_targets">
    <param name="targets_file" label="Targets File" type="data" format="data" optional="True" help="similar to -R but streams rather than index-jumps" />
    <param name="invert_targets_file" label="Invert Targets" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by the target file selection" />
  </xml>
  <xml name="macro_regions">
    <param name="regions_file" label="Regions File" type="data" format="data" optional="True" help="restrict to regions listed in a file" />
    <param name="invert_regions_file" label="Invert Regions" type="boolean" truevalue="^" falsevalue="" help="inverts the query/filtering applied by region file selection" />
  </xml>
  <xml name="macro_select_output_type">
    <param name="select_output_type" type="select">
      <option value="v" selected="True">uncompressed VCF</option>
      <option value="z">compressed VCF</option>
      <option value="u">uncompressed BCF</option>
      <option value="b">compressed BCF</option>
    </param>
  </xml>
</macros>