--- a/vegan_rarefaction.xml	Wed Dec 23 13:55:57 2015 -0500
+++ b/vegan_rarefaction.xml	Mon Feb 08 15:24:42 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.2">
+<tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.3">
     <description>
         curve and statistics
     </description>
@@ -32,24 +32,28 @@
 sprintf("Using sample size: %i", raremax)
 Srare <- rarefy(input_abundance, sample=raremax, se=FALSE, MARGIN=1)
 #if "output_richness" in $include_files:
-write.table(Srare, "${output_richness}", col.names=NA, sep = "\t")
+write.table(Srare, "${output_richness}", quote=FALSE, col.names=NA, sep = "\t")
 #end if
 
 #if "output_slope" in $include_files:
-write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", sep = "\t")
+write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", quote=FALSE, sep = "\t")
 #end if
 
 S <- specnumber(input_abundance)
 #if "output_species_count" in $include_files:
-write.table(S, "${ output_species_count }", col.names=NA, sep="\t" )
+write.table(S, "${ output_species_count }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_species_frequency" in $include_files:
-write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", col.names=NA, sep="\t" )
+write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_species_probabilities" in $include_files:
-write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", col.names=NA, sep="\t" )
+write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", quote=FALSE, col.names=NA, sep="\t" )
+#end if
+
+#if "output_random_rarefied" in $include_files:
+write.table( t( rrarefy(input_abundance, sample=raremax) ), "${ output_random_rarefied }", quote=FALSE, col.names=NA, sep="\t" )
 #end if
 
 #if "output_plot" in $include_files:
@@ -73,8 +77,9 @@
             <option value="output_richness" selected="true">Richness</option>
             <option value="output_species_probabilities" selected="true">Species probabilities</option>
             <option value="output_slope" selected="true">Slope of rarefaction curve</option>
+            <option value="output_plot" selected="true">Rarefaction plot</option>
+            <option value="output_random_rarefied" selected="true">Randomly rarefied community matrix</option>
             <option value="output_r_script" selected="false">R script</option>
-            <option value="output_plot" selected="true">Rarefaction plot</option>
         </param>
     </inputs>
     <outputs>
@@ -93,12 +98,15 @@
         <data format="tabular" name="output_slope" label="${tool.name} on ${on_string} (slope of curve)">
             <filter>"output_slope" in include_outputs</filter>
         </data>
+        <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
+            <filter>"output_plot" in include_outputs</filter>
+        </data>
+        <data format="tabular" name="output_random_rarefied" label="${tool.name} on ${on_string} (Random rarefied community matrix)">
+            <filter>"output_random_rarefied" in include_outputs</filter>
+        </data>
         <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)">
             <filter>"output_r_script" in include_outputs</filter>
         </data>
-        <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
-            <filter>"output_plot" in include_outputs</filter>
-        </data>
     </outputs>
     <tests>
         <test>