--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vegan_diversity.xml	Wed Aug 26 17:11:15 2015 -0400
@@ -0,0 +1,88 @@
+<tool id="vegan_diversity" name="Vegan Diversity" version="0.0.1">
+    <description>
+        index
+    </description>
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="2.3-0">vegan</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <command><![CDATA[
+        Rscript "${vegan_diversity_script}"
+    ]]>
+    </command>
+    <configfiles>
+        <configfile name="vegan_diversity_script"><![CDATA[
+#set $int_species_column = int( str( $species_column ) )
+#set $fixed_sample_columns = []
+#for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
+#assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
+#silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
+#end for
+library(vegan)
+input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
+input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
+
+write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
+    ]]>
+        </configfile>
+    </configfiles>
+    <inputs>
+        <param name="input_abundance" type="data" format="tabular" label="File with abundance values for community" help="Rows are samples; columns are species/phyla/community classifier"/>
+        <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
+        <param name="sample_columns" label="Sample count columns" type="data_column" multiple="True" value="2" data_ref="input_abundance" help="Select each column that contains counts"/>
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
+        <conditional name="index_type">
+            <param name="index_type_selector" type="select" label="Diversity index to use">
+                <option value="shannon" selected="True">shannon</option>
+                <option value="simpson">simpson</option>
+                <option value="invsimpson">invsimpson</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 used in shannon">
+                    <option value="exp(1)" selected="True">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 used in shannon">
+                    <option value="exp(1)" selected="True">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 used in shannon">
+                    <option value="exp(1)" selected="True">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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