# HG changeset patch
# User iuc
# Date 1710516408 0
# Node ID af1211ed6c8e949b29f3edd7846e8f06aeab8a92
# Parent  b0d5976540e35f2e5feab4141cbd6f885807841f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit f93edebf6c946402f105f0622aacb0baa216a70c

diff -r b0d5976540e3 -r af1211ed6c8e macros.xml
--- a/macros.xml	Fri Sep 07 11:31:02 2018 -0400
+++ b/macros.xml	Fri Mar 15 15:26:48 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 b0d5976540e3 -r af1211ed6c8e test-data/vegan_output_plot.png
Binary file test-data/vegan_output_plot.png has changed
diff -r b0d5976540e3 -r af1211ed6c8e 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 15:26:48 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 b0d5976540e3 -r af1211ed6c8e vegan_rarefaction.xml
--- a/vegan_rarefaction.xml	Fri Sep 07 11:31:02 2018 -0400
+++ b/vegan_rarefaction.xml	Fri Mar 15 15:26:48 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" />
@@ -109,7 +110,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="7">
             <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
             <param name="species_column" value="6"/>
             <param name="sample_columns" value="2"/>
@@ -123,6 +124,8 @@
             <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" />
             <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" />
             <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" />
+            <output name="output_plot" ftype="png" file="vegan_output_plot.png"  compare="sim_size" />
+            <output name="output_random_rarefied" ftype="tabular" file="vegan_output_random_rarefied.tabular" />
         </test>
     </tests>
     <help>
@@ -140,6 +143,5 @@
 When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1
         ]]>
     </help>
-    <citations>
-    </citations>
+    <expand macro="citations" />
 </tool>