--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.sim.xml	Fri May 19 05:21:12 2017 -0400
@@ -0,0 +1,153 @@
+<tool profile="16.07" id="mothur_heatmap_sim" name="Heatmap.sim" version="@WRAPPER_VERSION@.0">
+    <description>Generate a heatmap for pariwise similarity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$count" count.dat &&
+        #if $input.source == 'shared':
+            ln -s "$input.otu" input_otu.dat &&
+        #else
+            ln -s "$input.dist" input_dist.dat &&
+            #if $input.source == 'column':
+                ln -s "$input.name" input_name.dat &&
+            #end if
+        #end if
+
+        echo 'heatmap.sim(
+            #if $input.source == "shared":
+                shared=input_otu.dat,
+                #if $input.label:
+                    label=${ str($input.label).replace(",","-") },
+                #end if
+                #if $input.groups:
+                    groups=${ str($input.groups).replace(",","-") },
+                #end if
+                #if $input.calc:
+                    calc=${ str($input.calc).replace(",","-") },
+                #end if
+            #elif $input.source == "column":
+                column=input_dist.dat,
+                name=input_name.dat,
+            #elif $input.source == "phylip":
+                phylip=input_dist.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            fontsize=$fontsize
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="source" type="select" label="Generate Heatmap for">
+                <option value="shared">shared - Sample Similarity - OTU Shared</option>
+                <option value="phylip">phylip - Phylip Distance Matrix</option>
+                <option value="column">colomn - Pairwise Column Distance Matrix</option>
+            </param>
+            <when value="shared">
+                <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+                <param name="label" type="select" label="label - OTU Labels" multiple="true">
+                    <expand macro="labeloptions"/>
+                </param>
+                <param name="groups" type="select" multiple="true" label="groups - Groups to include">
+                    <options>
+                        <filter type="data_meta" ref="otu" key="groups"/>
+                    </options>
+                </param>
+                <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
+                    <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+                    <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+                    <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+                    <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+                    <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+                    <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+                    <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+                    <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+                    <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+                    <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
+                </param>
+            </when>
+            <when value="column">
+                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
+                <param name="name" type="data" format="mothur.names" label="name - Names"/>
+            </when>
+            <when value="phylip">
+                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+            </when>
+        </conditional>
+        <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg">
+            <filter>input['source'] != 'shared'</filter>
+        </data>
+        <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sim\.svg"/>
+            <filter>input['source'] == 'shared'</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="phylip"/>
+            <param name="dist" value="amazon.dist" ftype="mothur.square.dist"/>
+            <output name="heatmap">
+                <assert_contents>
+                    <has_text text="svg xmlns:svg="/>
+                    <has_text text="Heatmap for"/>
+                    <has_text text="U68640"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="source" value="shared"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output_collection name="heatmaps" count="72">
+                <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="source" value="shared"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.03,0.26,0.55"/>
+            <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
+            <param name="groups" value="forest,pasture"/>
+            <output_collection name="heatmaps" count="30">
+                <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
+
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
+
+v.1.24.0: Updated to Mothur 1.33, added count parameter
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>