--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/categorize_by_function.xml	Thu Dec 08 06:27:47 2016 -0500
@@ -0,0 +1,85 @@
+<tool id="picrust_categorize" name="Categorize by function" version="@WRAPPER_VERSION@.0">
+    <description>collapse hierarchical data to a specified level</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        categorize_by_function.py
+            -i '$input_fp'
+            -c $metadata_category
+            -l $level
+            -o tempbiom
+            $format_tab_delimited
+
+            @OUTPUT_CONVERSION_COMMANDS@
+    ]]></command>
+    <inputs>
+        <param argument="--input_fp" format="tabular,biom1" type="data" label="Input file" help="the output from the PICRISt predict tool"/>
+        <param argument="--metadata_category" type="select" multiple="false" label="Metadata category that describes the hierarchy" help="">
+            <option value="KEGG_Pathways" selected="true">KEGG Pathways</option>
+            <option value="COG_Category">COG Category</option>
+            <option value="taxonomy">Using taxonomy metadata</option>
+        </param>
+        <param argument="--level" type="integer" value="3" min="1" label="Hierarchy Level"
+               help="a value of 1 is the highest level, and any higher value nears the leaves of the hierarchy. For instance, if the hierarchy contains 4 levels, specifying 3 would collapse at one level above being fully specified"/>
+        <param argument="--format_tab_delimited" type="boolean" truevalue="-f" falsevalue="" checked="false" label="output the predicted metagenome table in tab-delimited" help="will contain the metadata lost in the classic output"/>
+        <expand macro="biom_format_select"/>
+    </inputs>
+    <outputs>
+        <expand macro="biom_output"/>
+        <data name="out_tabdel" format="tabular" from_work_dir="tempbiom" label="${tool.name} on ${on_string}: metagenome table">
+            <filter>format_tab_delimited</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test> <!-- test with Kegg Pathways and json output -->
+            <param name="input_fp" value="predicted_metagenomes.L3.biom"/>
+            <param name="metadata_category" value="KEGG_Pathways"/>
+            <param name="level" value="2"/>
+            <param name="format_tab_delimited" value="-f"/>
+            <param name="output_type" value="json"/>
+            <output name="out_biom" ftype="json">
+                <assert_contents>
+                    <has_text text="Biological Observation Matrix"/>
+                    <has_text text="generated_by"/>
+                    <has_text text="KEGG_Pathways"/>
+                    <has_text text="Cancers"/>
+                    <not_has_text text="ABC transporters"/>
+                </assert_contents>
+            </output>
+            <output name="out_tabdel" ftype="tabular" file="tempout.table"/>
+        </test>
+        <test> <!-- test with COG categories and classic output -->
+            <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/>
+            <param name="metadata_category" value="COG_Category"/>
+            <param name="level" value="1"/>
+            <param name="format_tab_delimited" value="-f"/>
+            <param name="output_type" value="tsv"/>
+            <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/>
+            <output name="out_tabdel" ftype="tabular" md5="e3545484ff53bf8650725573af2ebbb9"/>
+        </test>
+        <test> <!-- test with taxonomy metadata and hdf5 output -->
+            <param name="input_fp" value="observation_table.biom"/>
+            <param name="metadata_category" value="taxonomy"/>
+            <param name="level" value="1"/>
+            <param name="output_type" value="hdf5"/>
+            <output name="out_biom" ftype="hdf5" file="categorize_biom.hdf5" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+@PICRUST_OVERVIEW@
+
+**Command Documentation**
+
+This module collapses hierarchical data to a specified level for PICRUSt predictions. For instance, often it is useful to examine KEGG results from a higher level within the pathway hierarchy.
+Many genes are sometimes involved in multiple pathways, and in these circumstances (also know as a one-to-many relationship), the gene is counted for each pathway.
+
+**Input file:** Output file from the predict tool
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>