<macros>
    <token name="@TOOL_VERSION@">1.2.6</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">purge_dups</xref>
        </xrefs>
    </xml>
    <xml name="trimmers">
        <section name="section_hist" title="Histogram plot options" >
            <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
            <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
            <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
            <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
            <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
            <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
        </section>
    </xml>
    <token name="@HIST_PLOT@"><![CDATA[
        python '$__tool_directory__/hist_plot.py' 
        --cutoffs cutoffs.tsv
        #if $function_select.section_hist.ymin
            --ymin $function_select.section_hist.ymin
        #end if
        #if $function_select.section_hist.ymax
            --ymax $function_select.section_hist.ymax
        #end if
        #if $function_select.section_hist.xmin
            --xmin $function_select.section_hist.xmin
        #end if
        #if $function_select.section_hist.xmax
            --xmax $function_select.section_hist.xmax
        #end if
        #if $function_select.section_hist.title
            --title '${function_select.section_hist.title}'
        #end if
        depth.stat hist.png
    ]]></token>
    <token name="@CALCUTS@"><![CDATA[
        calcuts
        #if $function_select.section_calcuts.min_depth:
            -f $function_select.section_calcuts.min_depth
        #end if
        #if $function_select.section_calcuts.low_depth:
            -l $function_select.section_calcuts.low_depth
        #end if
        #if $function_select.section_calcuts.transition:
            -m $function_select.section_calcuts.transition
        #end if
        #if $function_select.section_calcuts.upper_depth:
            -u $function_select.section_calcuts.upper_depth
        #end if
        $function_select.section_calcuts.ploidy
    ]]></token>
    <xml name="calcuts">
        <section name="section_calcuts" title="Calcuts options" expanded="true">
            <param argument="-f" name="min_depth" type="float"  min="0" max="1" value="0.1" label="Minimum depth count fraction to maximum depth count"/>
            <param argument="-l" name="low_depth" type="integer" min="0" optional="true" label="Lower bound for read depth" />
            <param argument="-m" name="transition"  type="integer" min="0" optional="true" label="Transition between haploid and diploid"/>
            <param argument="-u" name="upper_depth"  type="integer"  min="0" optional="true" label="Upper bound for read depth" />
            <param name="ploidy" argument="-d" type="select" label="Ploidy" help="Treat as haploid assembly or diploid assembly">
                <option value="-d 0" selected="true">Diploid</option>
                <option value="-d 1">Haploid</option>
            </param>
        </section>
    </xml>
    <xml name="output_macro">
        <param name="output_options" type="select" multiple="true" display="checkboxes" label="Output files">
            <yield />
            <option value="histogram" selected="true">Histogram plot</option>
            <option value="calcuts_cutoff" selected="true">Calcuts cutoff</option>
            <option value="calcuts_log">Calcuts log</option>
        </param>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
            <requirement type="package" version="3.5.2">matplotlib-base</requirement>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/btaa025</citation>
        </citations>
    </xml>
</macros>