<macros>
    <token name="@TOOL_VERSION@">0.6.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.02</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="1.19.2">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>