--- a/compare_categories.xml	Mon Jul 10 16:47:19 2017 -0400
+++ b/compare_categories.xml	Sat Aug 05 07:20:31 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="qiime_compare_categories" name="Analyzes statistical significance" version="@WRAPPER_VERSION@.0">
-    <description>of sample groupings using distance matrices</description>
+<tool id="qiime_compare_categories" name="Analyze statistical significance of sample groupings" version="@WRAPPER_VERSION@.0">
+    <description> using distance matrices (compare_categories)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,18 +10,18 @@
     </expand>
     <version_command>compare_categories.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        compare_categories.py
-            --method '$method'
-            --input_dm '$input_dm'
-            --mapping_file '$mapping_file'
-            --categories '$categories'
-            -o compare_categories
-            #if $num_permutations
-                --num_permutations '$num_permutations'
-            #end if
-        ]]></command>
+compare_categories.py
+    --method '$method'
+    --input_dm '$input_dm'
+    --mapping_file '$mapping_file'
+    --categories '$categories'
+    -o compare_categories
+    #if $num_permutations
+        --num_permutations '$num_permutations'
+    #end if
+    ]]></command>
     <inputs>
-        <param argument="--method" label="Select the statistical method to use" type="select">
+        <param argument="--method" type="select" label="Select the statistical method to use">
             <option value="adonis">adonis</option>
             <option value="anosim">anosim</option>
             <option value="bioenv">bioenv</option>
@@ -34,7 +34,7 @@
         <param argument="--input_dm" type="data" format="txt,tabular,tsv" label="Input distance matrix" help="Only symmetric, hollow distance matrices may be used as input. Asymmetric distance matrices, such as those obtained by the UniFrac Gain metric (i.e. beta_diversity.py -m unifrac_g), should not be used as input"/>
         <param argument="--mapping_file" type="data" format="tabular,txt,tsv" label="Mapping file"/>
         <param argument="--categories" type="text" label="Comma-delimited list of categories from the mapping file" help="All methods except for BIO-ENV accept just a single category. If multiple categories are provided, only the first will be used"/>
-        <param argument="--num_permutations" type="integer" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero" optional="True" value="999" min="0"/>
+        <param argument="--num_permutations" type="integer" value="999" min="0" optional="True" label="Number of permutations to use when calculating statistical significance" help="Only applies to adonis, ANOSIM, MRPP, PERMANOVA, PERMDISP, and db-RDA. Must be greater than or equal to zero"/>
     </inputs>
     <outputs>
         <data name="test_results" format="txt" from_work_dir="compare_categories/*_results.txt" label="${tool.name} on ${on_string}: Test resuts"/>