--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cooccurrence.xml	Mon Oct 12 16:46:15 2015 -0400
@@ -0,0 +1,45 @@
+<tool id="cooccurrence" name="Cooccurrence" version="0.0.16">
+  <description>Taxonomic Co-occurrence Heatmap</description>
+  <requirements>
+    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="2014-05-02">microbiome_community</requirement>
+  </requirements>
+  <command interpreter="Rscript --vanilla">cooccurrence.R
+       #if str($CommunityFile).strip() != "":
+          --CommunityFile="$CommunityFile"
+       #end if
+       #if str($TaxonQuantile).strip() != "":
+          --TaxonQuantile="$TaxonQuantile"
+       #end if
+       #if str($Transform).strip() != "":
+          --Transform="$Transform"
+       #end if
+       #if str($OutputFile).strip() != "":
+          --OutputFile="$OutputFile"
+       #end if
+
+2&gt;&amp;1</command>
+  <inputs>
+    <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param optional="true" name="TaxonQuantile" type="float" value="0" help="(Optional, default 0) Numeric value between 0 and 1,&#10;limiting only taxa more frequent than the specified quantile." label="Taxon Quantile">
+      <validator type="empty_field" message="This field is required."/>
+    </param>
+    <param optional="true" name="Transform" type="select" help="(Optional; default 'none') Character string defining how&#10;count data are to be transformed prior to calculation of&#10;co-occurrence. Possible values are 'none', 'log1' (log of 1 +&#10;the observed count, to allow for zeros in the data), 'asinh'&#10;(a log-like transformation that handles zeros more&#10;naturally), 'sqrt' (square root, a transformation commonly&#10;used for count data)." label="Transform" force_select="FALSE">
+      <validator type="empty_field" message="This field is required."/>
+      <option value="none">none</option>
+      <option value="log1">log1</option>
+      <option value="asinh">asinh</option>
+      <option value="sqrt">sqrt</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="OutputFile" label="cooccurrence.pdf"/>
+  </outputs>
+  <help>
+**Description**
+
+Taxonomic co-occurrence across samples, displayed as a heatmap.
+</help>
+</tool>