--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make_otu_heatmap.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,167 @@
+<tool id="qiime_make_otu_heatmap" name="make otu heatmap" version="1.9.1galaxy1">
+    <description>Plot heatmap of OTU table</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command>
+<![CDATA[
+        make_otu_heatmap.py 
+            -i $otu_table_fp 
+            -o make_otu_heatmap_output
+
+            #if str($otu_tree) != 'None':
+             -t $otu_tree
+            #end if
+
+            #if str($map_fname) != 'None':
+             -m $map_fname
+            #end if
+
+            #if str($category):
+             -c $category
+            #end if
+
+            #if str($sample_tree) != 'None':
+             -s $sample_tree
+            #end if
+
+            #if $no_log_transform:
+             --no_log_transform
+            #end if
+
+            #if $suppress_row_clustering:
+             --suppress_row_clustering
+            #end if
+
+            #if $suppress_column_clustering:
+             --suppress_column_clustering
+            #end if
+
+            #if $absolute_abundance:
+             --absolute_abundance
+            #end if
+
+            #if str($ad.select) == "yes":
+                #if $ad.color_scheme:
+                    --color_scheme $ad.color_scheme
+                #end if
+
+                #if $ad.width:
+                    --width $ad.width
+                #end if
+
+                #if $ad.height:
+                    --height $ad.height
+                #end if
+
+                #if $ad.dpi:
+                    --dpi $ad.dpi
+                #end if
+
+                #if $ad.obs_md_category:
+                    --obs_md_category $ad.obs_md_category
+                #end if
+
+                #if $ad.obs_md_level:
+                    --obs_md_level $ad.obs_md_level
+                #end if
+            #end if
+]]>
+
+    </command>
+
+    <inputs>
+        <param label="-i/--otu_table_fp: path to the input OTU table (i.e., the 
+            output from make_otu_table.py)" name="otu_table_fp" optional="False" 
+            type="data"/>
+        <param default="None" label="-t/--otu_tree: Tree file to be used for 
+            sorting OTUs in the heatmap" name="otu_tree" optional="True" 
+            type="data"/>
+        <param default="None" label="-m/--map_fname: Metadata mapping file to be 
+            used for sorting Samples in the heatmap." name="map_fname" optional="True" 
+            type="data"/>
+        <param default="None" label="-c/--category: Metadata category for sorting 
+            samples. Samples will be clustered within each category level using 
+            euclidean UPGMA." name="category" optional="True" type="text"/>
+        <param default="None" label="-s/--sample_tree: Tree file to be used for 
+            sorting samples (e.g, output from upgma_cluster.py). If both this and 
+            the sample mapping file are provided, the mapping file is ignored." 
+            name="sample_tree" optional="True" type="data"/>
+        <param label="--no_log_transform: Data will not be log-transformed. 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." 
+            name="no_log_transform" selected="False" type="boolean"/>
+        <param label="--suppress_row_clustering: No UPGMA clustering of OTUs (rows) 
+            is performed. If --otu_tree is provided, this flag is ignored." 
+            name="suppress_row_clustering" selected="False" type="boolean"/>
+        <param label="--suppress_column_clustering: No UPGMA clustering of Samples 
+            (columns) is performed. If --map_fname is provided, this flag is ignored." 
+            name="suppress_column_clustering" selected="False" type="boolean"/>
+        <param label="--absolute_abundance: Do not normalize samples to sum to 1.
+            [default False]" name="absolute_abundance" selected="False" 
+            type="boolean"/>
+
+        <conditional name="ad">
+            <param name="select" type="select" label="Show advanced options">
+                <option value="no" selected="True">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param default="YlGn" label="Color scheme for figure. see http://matplotlib.org/examples/color/colormaps_reference.html for choices [default: YlGn]" 
+                    name="color_scheme" optional="True" type="text"/>
+                <param default="5" label="Width of the figure in inches [default: 5]" 
+                    name="width" optional="True" type="text"/>
+                <param default="5" label="Height of the figure in inches [default: 5]" 
+                    name="height" optional="True" type="text"/>
+                <param label="Resolution of the figure in dots per inch [default: 
+                    value of savefig.dpi in matplotlibrc file]" name="dpi" 
+                    optional="True" type="text"/>
+                <param label="Observation metadata category to plot [default: taxonomy]" 
+                    name="obs_md_category" optional="True" type="data"/>
+                <param label="The level of observation metadata to plot for hierarchical 
+                    metadata [default: lowest level]" name="obs_md_level" optional="True" 
+                    type="data"/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="pdf" from_work_dir="make_otu_heatmap_output" name="heatmap_OTU" 
+            label="heatmap_OTU.pdf"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+This script visualizes an OTU table as a heatmap where each row corresponds to an 
+OTU and each column corresponds to a sample. The higher the relative abundance of 
+an OTU in a sample, the more intense the color at the corresponsing position in 
+the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical 
+clustering, and the samples (columns) will be presented in the order in which 
+they appear in the OTU table. Alternatively, the user may supply a tree to sort 
+the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping 
+file for sorting samples. If the user passes in a mapping file and a metadata 
+category, samples (columns) will be grouped by category value and subsequently 
+clustered within each group.
+A single output file is created containing the heatmap of the OTU table (a PDF 
+file by default).
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>