--- a/categorize_by_function.xml	Thu Dec 08 06:27:47 2016 -0500
+++ b/categorize_by_function.xml	Wed Aug 30 04:49:00 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="picrust_categorize" name="Categorize by function" version="@WRAPPER_VERSION@.0">
-    <description>collapse hierarchical data to a specified level</description>
+<tool id="picrust_categorize" name="Categorize" version="@WRAPPER_VERSION@.0">
+    <description>by collapsing hierarchical data to a specified functional level</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,12 +11,11 @@
             -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="--input_fp" format="biom1,h5" type="data" label="Input file" help="Biom file that is 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>
@@ -24,23 +23,18 @@
         </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">
+            <output name="out_biom" ftype="biom1">
                 <assert_contents>
                     <has_text text="Biological Observation Matrix"/>
                     <has_text text="generated_by"/>
@@ -49,23 +43,20 @@
                     <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"/>
+            <output name="out_biom" ftype="h5" file="categorize_biom.hdf5" compare="sim_size"/>
         </test>
     </tests>
     <help>