--- a/bmsb.xml	Sun Aug 21 10:20:56 2016 -0400
+++ b/bmsb.xml	Thu Dec 15 11:04:41 2016 -0500
@@ -2,48 +2,58 @@
 <tool id="bmsb_model" name="Brown Marmorated Stink Bug" version="1.0.0">
     <description></description>
     <requirements>
-         <requirement type="package" version="3.3.1">r-base</requirement>
          <requirement type="package" version="1.3.0">r-optparse</requirement>
     </requirements>
     <command>
         <![CDATA[
-            #import json
-            Rscript $__tool_directory__/bmsb.R
-            -i "$input"
-            -o "$output"
-            ###if str($output_r_logging_cond.output_r_logging) == "yes":
-            ##    -s "true"
-            ##    -m "$output_r_log"
-            ###end if
-            ###if str($output_r_logging_cond.output_r_logging) == "yes":
-            ##    -e "true"
-            ##    -x "$output_ex_report"
-            ###end if
+            Rscript $__tool_directory__/BMSB.R
+            -adult_mort $adult_mort
+            -adult_nymph_accum $adult_nymph_accum
+            -egg_mort $egg_mort
+            -latitude $latitude
+            -location $location
+            -max_clutch_size $max_clutch_size
+            -min_clutch_size $min_clutch_size
+            -nymph_mort $nymph_mort
+            -old_nymph_accum $old_nymph_accum
+            -output $output
+            -oviposition $oviposition
+            -photoperiod $photoperiod
+            -replications $replications
+            -se_plot $se_plot
+            -sim_year $sim_year
+            -start_year $start_year
+            -temperature_datasets "$temperature_datasets"
+            -young_nymph_accum $young_nymph_accum
         ]]>
     </command>
     <inputs>
-        <param name="input" type="data" format="RData" label="RData input" />
-        <!--
-        <conditional name="output_r_logging_cond">
-            <param name="output_r_logging" type="select" label="Output R logging?" help="Generate an additional dataset consisting of R messages.">
-                <option value="yes" selected="True">Yes</option>
-                <option value="no">No</option>
-            </param>
-            <when value="no"/>
-            <when value="yes"/>
-        </conditional>
-        -->
+        <param name="location" type="select" label="Select a location">
+            <option value="asheville" selected=True>Asheville</option>
+            <option value="wenatchee">Wenatchee</option>
+        </param>
+        <param name="latitude" type="float" value="35.60" label="Latitude of selected location">
+        <param name="temperature_datasets" type="data" format="csv" multiple="true" label="Select datasets containing temperatures" help="One or more datasets can be selected"/>
+        <param name="start_year" type="integer" min="1990" label="Enter a starting year" />
+        <param name="replications" type="integer" value="3" label="Number of replications" />
+        <param name="photoperiod" type="float" value="13.5" label="Critical photoperiod for diapause induction/termination">
+        <param name="egg_mort" type="integer" label="Adjustment rate for egg mortality" />
+        <param name="nymph_mort" type="integer" label="Adjustment rate for nymph mortality" />
+        <param name="adult_mort" type="integer" label="Adjustment rate for adult mortality" />
+        <param name="oviposition" type="integer" label="Adjustment oviposition rate" />
+        <param name="min_clutch_size" type="integer" label="Adjustment of minimum clutch size" />
+        <param name="max_clutch_size" type="integer" label="Adjustment of maximum clutch size" />
+        <param name="young_nymph_accum" type="integer" label="Adjustment of DD accumulation (egg->young nymph)" />
+        <param name="old_nymph_accum" type="integer" label="Adjustment of DD accumulation (young nymph->old nymph)" />
+        <param name="adult_nymph_accum" type="integer" label="Adjustment of DD accumulation (old nymph->adult)" />
+        <param name="sim_year" type="integer" min="1990" label="Simulation year" />
+        <param name="se_plot" type="select" label="Plot SE?">
+            <option value="0" selected=True>No</option>
+            <option value="1">Yes</option>
+        </param>
     </inputs>
     <outputs>
-        <!--
-        <data name="output_r_log" format="txt" label="${tool.name} on ${on_string}: R log">
-            <filter>output_r_logging_cond['output_r_logging'] == "yes"</filter>
-        </data>
-        <data name="output_ex_report" format="json" label="${tool.name} on ${on_string}: Experiment report">
-            <filter>output_experiment_report_cond['output_experiment_report'] == "yes"</filter>
-        </data>
-        -->
-        <data name="output" format="RData"/>
+        <data name="output" format="RData" label="${tool.name}: ${location}, ${sim_year} on ${on_string}" />
     </outputs>
     <help>
 **What it does**