--- a/macros.xml	Fri Sep 07 11:30:36 2018 -0400
+++ b/macros.xml	Fri Mar 15 15:26:38 2024 +0000
@@ -36,6 +36,26 @@
 
 ]]>
     </token>
+    
+    <xml name="bio.tools_xrefs">
+        <xrefs>
+            <xref type="bio.tools">vegan</xref>
+        </xrefs>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @Manual{,
+                    title = {vegan: Community Ecology Package},
+                    author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
+                    year = {2024},
+                    note = {R package version 2.6-5},
+                    url = {https://github.com/vegandevs/vegan},
+                  }
+            </citation>
+        </citations>
+    </xml>
 
     <token name="@RSCRIPT_PREAMBLE@"><![CDATA[
 options(bitmapType='cairo')## No X11, so we'll use cairo

Binary file test-data/vegan_output_plot.png has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vegan_output_random_rarefied.tabular	Fri Mar 15 15:26:38 2024 +0000
@@ -0,0 +1,23 @@
+	V2
+        Bacteroidetes	4226
+        Chlorobi	10
+      Firmicutes	1163
+      Proteobacteria	402
+      Actinobacteria	275
+      Cyanobacteria	30
+        Acidobacteria	15
+        Fibrobacteres	8
+      Chloroflexi	12
+      Gemmatimonadetes	8
+      Aquificae	8
+      Tenericutes	7
+      Planctomycetes	6
+      Nitrospirae	5
+        Verrucomicrobia	5
+      Thermotogae	5
+      Fusobacteria	2
+      Deinococcus-Thermus	1
+      Elusimicrobia	1
+      Deferribacteres	1
+      Spirochaetes	1
+      Euryarchaeota	1

--- a/vegan_diversity.xml	Fri Sep 07 11:30:36 2018 -0400
+++ b/vegan_diversity.xml	Fri Mar 15 15:26:38 2024 +0000
@@ -5,6 +5,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio.tools_xrefs" />
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
@@ -57,7 +58,7 @@
         <data format="tabular" name="output_diversity_index" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
             <param name="species_column" value="6"/>
             <param name="sample_columns" value="2"/>
@@ -72,6 +73,5 @@
 Calculate Diversity index using vegan and selected method.
         ]]>
     </help>
-    <citations>
-    </citations>
+    <expand macro="citations" />
 </tool>