--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summarize_taxa.xml	Thu May 18 09:30:59 2017 -0400
@@ -0,0 +1,114 @@
+<tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
+    <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>summarize_taxa.py --version</version_command>
+    <command detect_errors="aggressive"><![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 argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table" help="(-i/)"/>
+        <param argument="--level" type="select" label="Taxonomic level to summarize by" 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 argument="--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" optional="True"/>
+        <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
+        <param argument="--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"/>
+        <param argument="--absolute_abundance" type="boolean" label="Report absolute abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" help="By default, relative abundance is reported"/>
+        <param argument="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" optional="True"/>
+        <param argument="--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" optional="True"/>
+        <param argument="--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"/>
+        <param argument="--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"/>
+        <param argument="--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"/>
+    </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="summarize_taxa/otu_table.biom"/>
+            <param name="level" value="2,3,4,5,6"/>
+            <param name="mapping" value="summarize_taxa/map.txt"/>
+            <param name="md_identifier" value="taxonomy"/>
+            <param name="md_as_string" 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/1_L2.txt"/>
+            <output name="L3_tab" value="summarize_taxa/1_L3.txt"/>
+            <output name="L4_tab" value="summarize_taxa/1_L4.txt"/>
+            <output name="L5_tab" value="summarize_taxa/1_L5.txt"/>
+            <output name="L6_tab" value="summarize_taxa/1_L6.txt"/>
+        </test>
+        <test>
+            <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
+            <param name="level" value="3,6"/>
+            <param name="md_identifier" value="taxonomy"/>
+            <param name="md_as_string" 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="L3_tab" value="summarize_taxa/2_L3.txt"/>
+            <output name="L6_tab" value="summarize_taxa/2_L6.txt"/>
+        </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>