# HG changeset patch
# User iuc
# Date 1710516398 0
# Node ID a1b80a746054c20f4f79e0f623ca8c834cb8c952
# Parent  a2c047a2c380aa5c85fbc02f5fd2238800cf05cd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit f93edebf6c946402f105f0622aacb0baa216a70c

diff -r a2c047a2c380 -r a1b80a746054 macros.xml
--- 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
diff -r a2c047a2c380 -r a1b80a746054 test-data/vegan_output_plot.png
Binary file test-data/vegan_output_plot.png has changed
diff -r a2c047a2c380 -r a1b80a746054 test-data/vegan_output_random_rarefied.tabular
--- /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
diff -r a2c047a2c380 -r a1b80a746054 vegan_diversity.xml
--- 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>