--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vegan_diversity.xml	Wed Dec 23 13:55:10 2015 -0500
@@ -0,0 +1,76 @@
+<tool id="vegan_diversity" name="Vegan Diversity" version="0.0.2">
+    <description>
+        index
+    </description>
+    <macros>
+        <import>vegan_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command><![CDATA[
+        Rscript "${vegan_diversity_script}"
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="vegan_diversity_script"><![CDATA[
+@RSCRIPT_PREAMBLE@
+@RSCRIPT_LOAD_TABULAR_FILE@
+
+write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
+    ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="params_load_tabular_file" />
+        <conditional name="index_type">
+            <param name="index_type_selector" type="select" label="Diversity index to use">
+                <option value="shannon" selected="True">Shannon or Shannon–Weaver (or Shannon–Wiener)</option>
+                <option value="simpson">Simpson</option>
+                <option value="invsimpson">Inverse Simpson</option>
+            </param>
+            <when value="shannon">
+                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
+                <param name="base" type="select" label="The logarithm base">
+                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
+                    <option value="2" selected="False">2</option>
+                </param>
+            </when>
+            <when value="simpson">
+                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
+                <param name="base" type="select" label="The logarithm base">
+                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
+                    <option value="2" selected="False">2</option>
+                </param>
+            </when>
+            <when value="invsimpson">
+                <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
+                <param name="base" type="select" label="The logarithm base">
+                    <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
+                    <option value="2" selected="False">2</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_diversity_index" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
+            <param name="species_column" value="6"/>
+            <param name="sample_columns" value="2"/>
+            <param name="index_type_selector" value="shannon"/>
+            <param name="margin" value="1"/>
+            <param name="base" value="exp(1)"/>
+            <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+Calculate Diversity index using vegan and selected method.
+        ]]>
+    </help>
+    <citations>
+    </citations>
+</tool>
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