--- a/mothur/tools/mothur/rarefaction.shared.xml	Wed May 16 13:12:05 2012 -0500
+++ b/mothur/tools/mothur/rarefaction.shared.xml	Tue Dec 04 11:05:19 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0">
+<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True">
  <description>Generate inter-sample rarefaction curves for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -12,6 +12,12 @@
   #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
   #end if
+  #if $design.use:
+   --design=$design.design
+   #if $design.sets.__str__ != '':
+    --sets='$design.sets'  
+   #end if
+  #end if
   #if int($iters.__str__) > 0:
    --iters=$iters
   #end if
@@ -19,6 +25,18 @@
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
     --calc='$calc'
   #end if
+  #if $subsample.use.__str__ == 'yes':
+   #if $subsample.subsample.__str__ != '':
+     --subsample=$subsample.subsample
+   #else
+     --subsample=T
+   #end if
+   #if $subsample.subsampleiters.__str__ != '':
+     --subsampleiters=$subsample.subsampleiters
+   #end if
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular'
+  #end if
  </command>
  <inputs>
   <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
@@ -31,22 +49,48 @@
    <help>All groups will be analyzed by default if none are selected</help>
    <options>
     <filter type="data_meta" ref="otu" key="groups" />
+    <!--
     <filter type="add_value" name="all" value="all" />
+    -->
    </options>
   </param>
+  <conditional name="design">
+    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label=" run on a per set basis using a design file"/>
+    <when value="yes">
+    <param name="design" type="data" format="design" label="design - assigns groups to sets" 
+           help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
+    <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
+     <options>
+      <filter type="data_meta" ref="design" key="groups" />
+     </options>
+    </param>
+    </when>
+    <when value="no"/>
+  </conditional>
+
   <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
   <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
    <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
    <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
   </param>
+  <conditional name="subsample">
+    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample rarefactions"/>
+    <when value="yes">
+      <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" 
+             help="Leave blank to use the size of your smallest group"/>
+      <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
+    </when>
+    <when value="no"/>
+  </conditional>
+
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.27">mothur</requirement>
  </requirements>
  <tests>
  </tests>