<tool id="qiime_plot_taxa_summary" name="Make taxonomy summary charts" version="1.9.1">
    <description>based on taxonomy assignment</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <version_command><![CDATA[
        plot_taxa_summary.py --version
    ]]>
    </version_command>

    <command>
<![CDATA[
        #set $chosen_chart_type = str( $chart_type ).split( "," )

        plot_taxa_summary.py 
            -i $counts_fname 

            -o taxa_plots

            #if str($labels):
                -l $labels
            #end if

            -n $num_categories

            #if str( $colorby)
                -b $colorby
            #end if

            -k $background_color
            -d $dpi
            -x $x_width
            -y $y_height
            -w $bar_width

            -c $chart_type
            $include_html_legend
            -a $label_type

        #if "area" in $chosen_chart_type:
            &&
            mkdir -p $area_charts_html_report.files_path 
            &&
            cp -r taxa_plots/area_charts.html $area_charts_html_report.files_path  
            &&
            cp -r taxa_plots/charts $area_charts_html_report.files_path  
            &&
            cp -r taxa_plots/css $area_charts_html_report.files_path  
            &&
            cp -r taxa_plots/js $area_charts_html_report.files_path  
            && 
            mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
        #end if

        #if "bar" in $chosen_chart_type:
            &&
            mkdir -p $bar_charts_html_report.files_path 
            &&
            cp -r taxa_plots/bar_charts.html $bar_charts_html_report.files_path  
            &&
            cp -r taxa_plots/charts $bar_charts_html_report.files_path  
            &&
            cp -r taxa_plots/css $bar_charts_html_report.files_path  
            &&
            cp -r taxa_plots/js $bar_charts_html_report.files_path  
            && 
            mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
        #end if

        #if "pie" in $chosen_chart_type:
            &&
            mkdir -p $pie_charts_html_report.files_path 
            &&
            cp -r taxa_plots/pie_charts.html $pie_charts_html_report.files_path  
            &&
            cp -r taxa_plots/charts $pie_charts_html_report.files_path  
            &&
            cp -r taxa_plots/css $pie_charts_html_report.files_path  
            &&
            cp -r taxa_plots/js $pie_charts_html_report.files_path  
            && 
            mv $pie_charts_html_report.files_path/pie_charts.html $pie_charts_html_report
        #end if
]]>
    </command>

    <inputs>
        <param name="counts_fname" type="data" format="tabular,txt,tsv" 
            label="Summarized taxa files" multiple="True" 
            help="(-i/--counts_fname)"/> 

        <param name="labels" type="text" value="" label="Comma-separated list of
            taxonomic levels (optional)"  help="(-l/--labels)" optional="True"/>

        <param name="num_categories" type="integer" value="20" label="Maximum 
            number of taxonomies to show in each pie chart" help="All additional 
            taxonomies are grouped into an 'other' category. This functionality 
            only applies to the pie charts(-n/--num_categories)"/>

        <param name="colorby" type="text" value="" label="Categories to color
            by in the plots from the metadata mapping file (optional)" 
            help="The categories must match the name of a column header in the 
            mapping file exactly and multiple categories can be list by comma 
            separating them without spaces(-b/--colorby)" optional="True"/>

        <param name="background_color" type="select" label="Background color to 
            use in the plots" help="(-k/--background_color)">
            <option value="white">White</option>
            <option value="black">Black</option>
        </param>

        <param name="dpi" type="integer" value="80" label="Resolution of the plot" 
            help="(-d/--dpi)"/>

        <param name="x_width" type="integer" value="12" label="Width of the 
            x-axis to use in the plots" help="(-x/--x_width)"/>

        <param name="y_height" type="integer" value="12" label="Height of the 
            y-axis to use in the plots" help="(-y/--y_height)"/>

        <param name="bar_width" type="float" value="0.75" min="0" maw="1" 
            label="Width of the bars in the bar graph" help="(-w/--bar_width)"/>

        <param name="chart_type" type="select" label="Type of chart to plot" 
            help="(-c/--chart_type)" multiple="True" display="checkboxes">
            <option value="area" selected="true">Area</option>
            <option value="bar" selected="true">Bar</option>
            <option value="pie">Pie</option>
        </param>

        <param name="include_html_legend" type="boolean" label="Include HTML 
            legend?" truevalue="--include_html_legend" falsevalue="" checked="False" 
            help="If checked, the writing of the legend in the html page is 
            included (-s/--include_html_legend)" />

        <param name="label_type" type="select" label="Label type" 
            help="If the label type is defined as numeric, the x-axis will be 
            scaled accordingly. Otherwise the x-values will treated categorically 
            and be evenly spaced(-a/--label_type)">
            <option value="categorical" selected="true">Categorical</option>
            <option value="numeric">Numeric</option>
        </param>
    </inputs>

    <outputs>
        <data name="bar_charts_html_report" format="html" 
            label="${tool.name} on ${on_string}: Bar charts">
            <filter>'bar' in chart_type</filter>
        </data>
        <data name="pie_charts_html_report" format="html" 
            label="${tool.name} on ${on_string}: Pie charts">
            <filter>'pie' in chart_type</filter>
        </data>
        <data name="area_charts_html_report" format="html" 
            label="${tool.name} on ${on_string}: Area charts">
            <filter>'area' in chart_type</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="counts_fname"
                value="summarize_taxa_L2.tab"/> 
            <param name="num_categories" value="20"/>
            <param name="background_color" value="white"/>
            <param name="dpi" value="80" />
            <param name="x_width" value="12" />
            <param name="y_height" value="12" />
            <param name="bar_width" value="0.75" />
            <param name="chart_type" value="area,bar"/>
            <param name="include_html_legend" value=""  />
            <param name="label_type" value="categorical"/>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

This script automates the construction of pie, bar and area charts showing the breakdown of taxonomy by given levels.

More information about this tool is available on 
`QIIME documentation <http://qiime.org/scripts/plot_taxa_summary.html>`_.
    ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>