--- a/make_otu_heatmap.xml	Mon Jul 10 16:40:04 2017 -0400
+++ b/make_otu_heatmap.xml	Sat Aug 05 07:32:00 2017 -0400
@@ -1,69 +1,69 @@
 <tool id="qiime_make_otu_heatmap" name="Plot heatmap of OTU table" version="@WRAPPER_VERSION@.0">
-    <description></description>
+    <description>(make_otu_heatmap)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>make_otu_heatmap.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        make_otu_heatmap.py
-            --otu_table_fp '$otu_table_fp'
+make_otu_heatmap.py
+    --otu_table_fp '$otu_table_fp'
 
-            #if $imagetype == "pdf"
-                --output_fp '$pdf_output_fp'
-            #else if $imagetype == "png"
-                --output_fp '$png_output_fp'
-            #else if $imagetype == "svg"
-                --output_fp '$svg_output_fp'
-            #end if
+    #if $imagetype == "pdf"
+        --output_fp '$pdf_output_fp'
+    #else if $imagetype == "png"
+        --output_fp '$png_output_fp'
+    #else if $imagetype == "svg"
+        --output_fp '$svg_output_fp'
+    #end if
 
-            #if $otu_tree
-                --otu_tree '$otu_tree'
-            #end if
-            #if $map_fname
-                --map_fname '$map_fname'
-            #end if
-            #if str($category) != ''
-                --category '$category'
-            #end if
-            #if $sample_tree
-                --sample_tree '$sample_tree'
-            #end if
-            --imagetype '$imagetype'
-            $no_log_transform
-            $suppress_row_clustering
-            $suppress_column_clustering
-            $absolute_abundance
+    #if $otu_tree
+        --otu_tree '$otu_tree'
+    #end if
+    #if $map_fname
+        --map_fname '$map_fname'
+    #end if
+    #if str($category) != ''
+        --category '$category'
+    #end if
+    #if $sample_tree
+        --sample_tree '$sample_tree'
+    #end if
+    --imagetype '$imagetype'
+    $no_log_transform
+    $suppress_row_clustering
+    $suppress_column_clustering
+    $absolute_abundance
 
-            #if str($ad.select) == "yes":
-                --color_scheme '$ad.color_scheme'
-                --width '$ad.width'
-                --height '$ad.height'
-                --dpi '$ad.dpi'
-                --obs_md_category '$ad.obs_md_category'
-                #if str($ad.obs_md_level) != ''
-                    --obs_md_level '$ad.obs_md_level'
-                #end if    
-            #end if
+    #if str($ad.select) == "yes":
+        --color_scheme '$ad.color_scheme'
+        --width '$ad.width'
+        --height '$ad.height'
+        --dpi '$ad.dpi'
+        --obs_md_category '$ad.obs_md_category'
+        #if str($ad.obs_md_level) != ''
+            --obs_md_level '$ad.obs_md_level'
+        #end if
+    #end if
     ]]></command>
     <inputs>
         <param argument="--otu_table_fp" type="data" format="biom1" label="Input OTU table"/>
-        <param argument="--otu_tree" type="data" format="txt" label="Tree file to be used for sorting OTUs in the heatmap" name="otu_tree" optional="True"/>
-        <param argument="--map_fname" type="data" format="txt" label="Metadata mapping file to be used for sorting" optional="True"/>
-        <param argument="--category" type="text" label="Metadata category for sorting samples" help=" Samples will be clustered within each category level using euclidean UPGMA" optional="True"/>
-        <param argument="--sample_tree" type="data" format="txt" label="Tree file to be used for sorting samples" help="If both this and the sample mapping file are provided, the mapping file is ignored." optional="True"/>
+        <param argument="--otu_tree" type="data" format="txt" optional="true" label="Tree file to be used for sorting OTUs in the heatmap"/>
+        <param argument="--map_fname" type="data" format="txt" optional="true" label="Metadata mapping file to be used for sorting"/>
+        <param argument="--category" type="text" optional="True" label="Metadata category for sorting samples" help=" Samples will be clustered within each category level using euclidean UPGMA"/>
+        <param argument="--sample_tree" type="data" format="txt" optional="true" label="Tree file to be used for sorting samples" help="If both this and the sample mapping file are provided, the mapping file is ignored."/>
         <param argument="--imagetype" type="select" label="Type of image to produce">
-            <option value="pdf" selected="True">PDF</option>
+            <option value="pdf" selected="true">PDF</option>
             <option value="png">PNG</option>
             <option value="svg">SVG</option>
         </param>
-        <param argument="--no_log_transform" type="boolean" truevalue="--no_log_transform" falsevalue="" checked="False" label="Data will not be log-transformed the data?" help="Without this option, all zeros will be set to a small value (default is 1/2 the smallest non-zero entry). Data will be translated to be non-negative after log transform, and num_otu_hits will be set to 0."/>
-        <param argument="--suppress_row_clustering" type="boolean" truevalue="--suppress_row_clustering" falsevalue="" checked="False" label="Perform no UPGMA clustering of OTUs (rows)?" help="If --otu_tree is provided, this flag is ignored."/>
-        <param argument="--suppress_column_clustering" type="boolean" truevalue="--suppress_column_clustering" falsevalue="" checked="False" label="Perform no UPGMA clustering of Samples (columns)?" help="If --map_fname is provided, this flag is ignored."/>
-        <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="False" label="Do not normalize samples to sum to 1?"/>
+        <param argument="--no_log_transform" type="boolean" truevalue="--no_log_transform" falsevalue="" checked="false" label="Data will not be log-transformed the data?" help="Without this option, all zeros will be set to a small value (default is 1/2 the smallest non-zero entry). Data will be translated to be non-negative after log transform, and num_otu_hits will be set to 0."/>
+        <param argument="--suppress_row_clustering" type="boolean" truevalue="--suppress_row_clustering" falsevalue="" checked="false" label="Perform no UPGMA clustering of OTUs (rows)?" help="If --otu_tree is provided, this flag is ignored."/>
+        <param argument="--suppress_column_clustering" type="boolean" truevalue="--suppress_column_clustering" falsevalue="" checked="false" label="Perform no UPGMA clustering of Samples (columns)?" help="If --map_fname is provided, this flag is ignored."/>
+        <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Do not normalize samples to sum to 1?"/>
         <conditional name="ad">
             <param name="select" type="select" label="Show advanced options">
-                <option value="no" selected="True">No</option>
+                <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>