--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_taxa_summary.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,194 @@
+<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>