--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_taxa_through_plots.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,140 @@
+<tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="1.9.1">
+    <description>summaries and plots</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        summarize_taxa_through_plots.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        summarize_taxa_through_plots.py 
+            -i $otu_table_fp 
+            -o summarize_taxa_through_plots
+
+            #if $mapping_fp
+                -m $mapping_fp
+            #end if
+
+            #if $mapping_category
+                -c $mapping_category
+            #end if
+
+            $sort
+        
+        &&
+
+        mkdir -p $area_charts_html_report.files_path 
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/area_charts.html $area_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $area_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/css $area_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/js $area_charts_html_report.files_path  
+        && 
+        mv $area_charts_html_report.files_path/area_charts.html $area_charts_html_report
+    
+        &&
+        mkdir -p $bar_charts_html_report.files_path 
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/bar_charts.html $bar_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/charts $bar_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/css $bar_charts_html_report.files_path  
+        &&
+        cp -r summarize_taxa_through_plots/taxa_summary_plots/js $bar_charts_html_report.files_path  
+        && 
+        mv $bar_charts_html_report.files_path/bar_charts.html $bar_charts_html_report
+        
+]]>
+    </command>
+
+    <inputs>
+        <param name="otu_table_fp" type="data" format="biom,tabular,txt,tsv" 
+            label="Input OTU table" help="(-i/--otu_table_fp)"/> 
+
+        <param name="mapping_fp" type="data" format="tabular,tsv,csv" 
+            label="Input metadata mapping (optional)" help="(-m, --mapping_fp)" 
+            optional="True"/>
+
+        <param name="mapping_category" type="text" value="" label="Category to 
+            use to summarize OTU table"  help="(-c/--mapping_category)" 
+            optional="True"/>
+
+        <param name="sort" type="boolean" label="Sort OTU table?" 
+            truevalue="--sort" falsevalue="" selected="False" 
+            help="(-s/--sort)" />
+    </inputs>
+
+    <outputs>
+        <data name="L2_tab" format="tabular" 
+            from_work_dir="summarize_taxa_through_plots/*_L2.txt" 
+            label="${tool.name} on ${on_string}: L2 tab">
+            <filter>"2" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L3_tab" format="tabular" 
+            from_work_dir="summarize_taxa_through_plots/*_L3.txt" 
+            label="${tool.name} on ${on_string}: L3 tab">
+            <filter>"3" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L4_tab" format="tabular" 
+            from_work_dir="summarize_taxa_through_plots/*_L4.txt" 
+            label="${tool.name} on ${on_string}: L4 tab">
+            <filter>"4" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L5_tab" format="tabular" 
+            from_work_dir="summarize_taxa_through_plots/*_L5.txt" 
+            label="${tool.name} on ${on_string}: L5 tab">
+            <filter>"5" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L6_tab" format="tabular" 
+            from_work_dir="summarize_taxa_through_plots/*_L6.txt" 
+            label="${tool.name} on ${on_string}: L6 tab">
+            <filter>"6" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="bar_charts_html_report" format="html" 
+            label="${tool.name} on ${on_string}: Bar charts">
+            <filter>'bar' is chart_type</filter>
+        </data>
+
+        <data name="area_charts_html_report" format="html" 
+            label="${tool.name} on ${on_string}: Area charts">
+            <filter>'area' is chart_type</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool summarizes OTU by Category (optional), summarizes taxonomy and plots
+taxonomy summary.
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/summarize_taxa_through_plots.html>`_.
+]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+
+</tool>