<macros>
  <token name="@TOOL_VERSION@">0.5.0</token>
  <token name="@VERSION_SUFFIX@">2</token>
  <token name="@PROFILE@">21.05</token>

  <token name="@THREADS@"><![CDATA[
      ##compute the number of ADDITIONAL threads to be used by samtools (-@)
      addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
  ]]></token>

  <xml name="version_command">
     <version_command><![CDATA[polypolish -V]]></version_command>
  </xml>
  <xml name="xrefs">
    <xrefs>
      <xref type='bio.tools'>Polypolish</xref>
    </xrefs>
  </xml>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">polypolish</requirement>
      <requirement type="package" version="1.19">samtools</requirement>
    </requirements>
  </xml>
  <xml name="citations">
      <citations>
          <citation type="doi">10.1371/journal.pcbi.1009802</citation>
      </citations>
  </xml>
  <!-- Filter option of polypolish -->
  <xml name="filter_option">
      <conditional name="insert_filter">
          <param name="filter_select" type="select" label="Filter by insert size ? [recommanded]"
                 help="Exclude some alignments based on their insert size. It reduce the number of excessive alignments,
                 particularly near the edges of repeat sequences">
              <option value="filter" selected="true">Filter by insert size</option>
              <option value="non_filter"> No filtering step</option>
          </param>
          <when value="filter">
              <param argument="--low" type="float" min="0" value="0.1" label="Low percentile threshold" help="Select the lower value to remove [default: 0.1]"/>
              <param argument="--high" type="float" min="0" value="99.9" label="High percentile threshold" help="Select the lower value to remove [default: 99.9]"/>
          </when>
          <when value="non_filter">
          </when>
      </conditional>
  </xml>
</macros>