--- a/beta_diversity.xml	Mon Jul 10 16:37:06 2017 -0400
+++ b/beta_diversity.xml	Fri Aug 04 18:16:17 2017 -0400
@@ -1,5 +1,5 @@
 <tool id="qiime_beta_diversity" name="Calculate beta diversity" version="@WRAPPER_VERSION@.0">
-    <description>pairwise sample dissimilarity</description>
+    <description>(pairwise sample dissimilarity) on one or many otu tables (beta_diversity)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -9,21 +9,21 @@
     </stdio>
     <version_command>beta_diversity.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        #set $chosen_metrics = str( $metrics ).split( "," )
-        beta_diversity.py
-            --input_path '$input_path'
-            #if $rows
-                --rows '$rows'
-            #end if
-            -o beta_diversity
-            --metrics '$metrics'
-            #if ("unifrac_g" in $chosen_metrics or "unifrac_g_full_tree" in $chosen_metrics or "unweighted_unifrac" in $chosen_metrics or "unweighted_unifrac_full_tree" in $chosen_metrics or "weighted_normalized_unifrac" in $chosen_metrics or "weighted_unifrac" in $chosen_metrics) and $tree_path
-                --tree_path '$tree_path'
-            #end if
-            $full_tree
+#set $chosen_metrics = str( $metrics ).split( "," )
+beta_diversity.py
+    --input_path '$input_path'
+    #if $rows
+        --rows '$rows'
+    #end if
+    -o beta_diversity
+    --metrics '$metrics'
+    #if ("unifrac_g" in $chosen_metrics or "unifrac_g_full_tree" in $chosen_metrics or "unweighted_unifrac" in $chosen_metrics or "unweighted_unifrac_full_tree" in $chosen_metrics or "weighted_normalized_unifrac" in $chosen_metrics or "weighted_unifrac" in $chosen_metrics) and $tree_path
+        --tree_path '$tree_path'
+    #end if
+    $full_tree
     ]]></command>
     <inputs>
-        <param argument="--input_path" type="data" format="tabular,txt,tsv" label="OTU table" help=""/>
+        <param argument="--input_path" type="data" format="tabular,txt,tsv" label="OTU table"/>
         <param argument="--rows" type="text" value="" optional="true" label="Rows on which distance matrix is computed (optional)" help="A comma-separated list of sample names is expected"/>
         <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Beta-diversity metric(s) to use">
             <option value="abund_jaccard">Abundance weighted Jaccard distance</option>
@@ -57,8 +57,8 @@
             <option value="weighted_normalized_unifrac">Normalized weighted UniFrac metric (phylogenetic)</option>
             <option value="weighted_unifrac" selected="true">Weighted UniFrac metric (phylogenetic)</option>
         </param>
-        <param argument="--tree_path" type="data" format="nhx,txt" optional="True" label="Newick tree (optional, except for PD_whole_tree metric)"/>
-        <param argument="--full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="False" label="Skip the removal of tips not corresponding to OTUs in the OTU table from the tree for diversity calculations?" help="By default, tips not corresponding to OTUs in the OTU table are removed from the tree for diversity calculations. Pass to skip this step if you’re already passing a minimal tree. Beware with 'full_tree' metrics, as extra tips in the tree change the result"/>
+        <param argument="--tree_path" type="data" format="nhx,txt" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/>
+        <param argument="--full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="Skip the removal of tips not corresponding to OTUs in the OTU table from the tree for diversity calculations?" help="By default, tips not corresponding to OTUs in the OTU table are removed from the tree for diversity calculations. Pass to skip this step if you’re already passing a minimal tree. Beware with 'full_tree' metrics, as extra tips in the tree change the result"/>
     </inputs>
     <outputs>
         <collection name="beta_diversity" type="list" label="${tool.name} on ${on_string}: Beta diversity metrics">