--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_taxa.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,186 @@
+<tool id="qiime_summarize_taxa" name="Summarize taxa" version="1.9.1">
+    <description>and store results in a new table or appended to an existing 
+        mapping file
+    </description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        summarize_taxa.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        summarize_taxa.py 
+            -i $otu_table_fp
+            -o summarize_taxa
+
+            -L $level
+
+            #if str($mapping) != 'None':
+                -m $mapping
+            #end if
+
+            --md_identifier $md_identifier
+
+            $md_as_string
+
+            $absolute_abundance
+
+            #if str( $lower_percentage )
+                -l $lower_percentage
+            #end if
+
+            #if str( $upper_percentage)
+                -u $upper_percentage
+            #end if
+
+            $transposed_output             
+            $suppress_classic_table_output
+            $suppress_biom_table_output
+]]>
+    </command>
+
+    <inputs>
+        <param name="otu_table_fp" type="data" format="tabular,tsv,txt,biom" 
+            label="Input OTU table" help="(-i/--otu_table_fp)"/> 
+
+        <param name="level" type="select" label="Taxonomic level to summarize by"
+            help="(-L/--level)" multiple="True" display="checkboxes">
+            <option value="1" >Kingdom</option>
+            <option value="2" selected="true">Phylum</option>
+            <option value="3" selected="true">Class</option>
+            <option value="4" selected="true">Order</option>
+            <option value="5" selected="true">Family</option>
+            <option value="6" selected="true">Genus</option>
+            <option value="7" >Species</option>
+        </param>
+
+        <param name="mapping" type="data" format="tabular,tsv,csv" 
+            label="Input metadata mapping (optional)" help="If supplied, then the 
+            taxon information will be added to this file. This option is useful for 
+            coloring PCoA plots by taxon abundance or to perform statistical 
+            tests of taxon/mapping associations (-m/--mapping)" optional="True"/>
+
+        <param name="md_identifier" type="text" value="taxonomy" label="Relevant 
+            observation metadata key"  help="(--md_identifier)" />
+
+        <param name="md_as_string" type="boolean" label="Include metadata as string?" 
+            truevalue="--md_as_string" falsevalue="" checked="False" 
+            help="By default, metadata is included as list (--md_as_string)" />
+
+        <param name="absolute_abundance" type="boolean" label="Report absolute
+            abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" 
+            help="By default, relative abundance is reported (--absolute_abundance)" />
+
+        <param name="lower_percentage" type="float" label="Percentage threshold to
+            remove highly present OTU (optional)" help="If present, OTUs having 
+            higher absolute abundance are trimmed. To remove OTUs that make up 
+            more than 5% of the total dataset you would pass 0.05 (-l/--lower_percentage)" 
+            optional="True"/>
+
+        <param name="upper_percentage" type="float" label="Percentage threshold to
+            remove lowly present OTU (optional)" help="If present, OTUs having 
+            lower absolute abundance are trimmed. To remove the OTUs that 
+            makes up less than 45% of the total dataset you would pass 0.45 
+            (-u/--upper_percentage)" optional="True"/>
+
+        <param name="transposed_output" type="boolean" label="Transpose output?" 
+            truevalue="--transposed_output" falsevalue="" checked="False" 
+            help="If checked, the output will be written transposed from the 
+            regular output. This is helpful in cases when you want to use Site 
+            Painter to visualize your data (-t/--transposed_output)" />
+
+        <param name="suppress_classic_table_output" type="boolean" 
+            label="Suppress creation of the classic (TSV) format taxon table?" 
+            truevalue="--suppress_classic_table_output" falsevalue="" checked="False" 
+            help="This option is ignored if a mapping file is present 
+            (--suppress_classic_table_output)" />
+
+        <param name="suppress_biom_table_output" type="boolean" 
+            label="Suppress creation of the BIOM-formatted taxon table?" 
+            truevalue="--suppress_biom_table_output" falsevalue="" checked="False" 
+            help="This option is ignored if a mapping file is present 
+            (--suppress_biom_table_output)" />
+    </inputs>
+
+    <outputs>
+        <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" 
+            label="${tool.name} on ${on_string}: L1 tab">
+            <filter>"1" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" 
+            label="${tool.name} on ${on_string}: L2 tab">
+            <filter>"2" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" 
+            label="${tool.name} on ${on_string}: L3 tab">
+            <filter>"3" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" 
+            label="${tool.name} on ${on_string}: L4 tab">
+            <filter>"4" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" 
+            label="${tool.name} on ${on_string}: L5 tab">
+            <filter>"5" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" 
+            label="${tool.name} on ${on_string}: L6 tab">
+            <filter>"6" in level and suppress_classic_table_output is False</filter>
+        </data> 
+
+        <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" 
+            label="${tool.name} on ${on_string}: L7 tab">
+            <filter>"7" in level and suppress_classic_table_output is False</filter>
+        </data> 
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="otu_table_fp" 
+                value="pick_open_reference_otus_otu_table_with_taxo.biom"/> 
+            <param name="level" value="2,3,4,5,6" />
+            <param name="mapping" 
+                value="validate_mapping_file_corrected_map.tabular"/>
+            <param name="md_identifier" value="taxonomy"/>
+            <param name="md_as_string" value=""/>
+            <param name="delimiter" value=";" />
+            <param name="absolute_abundance" value=""/>
+            <param name="transposed_output" value=""/>
+            <param name="suppress_classic_table_output" value="" />
+            <param name="suppress_biom_table_output" value="" /> 
+
+            <output name="L2_tab" value="summarize_taxa_L2.tabular" /> 
+            <output name="L3_tab" value="summarize_taxa_L3.tabular" /> 
+            <output name="L4_tab" value="summarize_taxa_L4.tabular" /> 
+            <output name="L5_tab" value="summarize_taxa_L5.tabular" /> 
+            <output name="L6_tab" value="summarize_taxa_L6.tabular" /> 
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+This tool provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input. 
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>