--- a/insect_phenology_model.xml	Tue Dec 05 11:32:33 2017 -0500
+++ b/insect_phenology_model.xml	Tue Dec 05 15:15:49 2017 -0500
@@ -5,23 +5,24 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/insect_phenology_model.R'
--a $adult_mortality
--b $adult_accumulation
--c $egg_mortality
--e '$location'
--f $max_clutch_size
--i $min_clutch_size
--j $nymph_mortality
--k $old_nymph_accumulation
--n $input.metadata.data_lines
--o '$output'
--p $oviposition
--q $photoperiod
--s $replications
--t $std_error_plot
--v '$input'
--y $young_nymph_accumulation
--x '$insect']]></command>
+--adult_mortality $adult_mortality
+--adult_accumulation $adult_accumulation
+--egg_mortality $egg_mortality
+--input '$input'
+--insect '$insect'
+--insects_per_replication $insects_per_replication
+--location '$location'
+--max_clutch_size $max_clutch_size
+--min_clutch_size $min_clutch_size
+--nymph_mortality $nymph_mortality
+--num_days $input.metadata.data_lines
+--old_nymph_accumulation $old_nymph_accumulation
+--output '$output'
+--oviposition $oviposition
+--photoperiod $photoperiod
+--replications $replications
+--std_error_plot $std_error_plot
+--young_nymph_accumulation $young_nymph_accumulation]]></command>
     <inputs>
         <param name="input" type="data" format="csv" label="Temperature data" />
         <param name="location" type="text" value="" optional="false" label="Location" />
@@ -29,6 +30,7 @@
             <option value="Brown Marmolated Stink Bug" selected="True">Brown Marmolated Stink Bug</option>
         </param>
         <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
+        <param name="insects_per_replication" type="integer" value="1000" min="1" label="Number of insects with which to start each replication" />
         <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
         <param name="egg_mortality" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
         <param name="nymph_mortality" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
@@ -66,7 +68,9 @@
 
  * **Location** - the location associated with the selected temperature data.
  * **Temperature data** - select the dataset from your history containing the temperature data.
+ * **Select insect** - currently only the Brown Marmolated Stink Bug can be analyzed.
  * **Number of replications** - number of replications.
+ * **Number of insects with which to start each replication** - the analysis for each replication will start with this number of insects.
  * **Critical photoperiod for diapause induction/termination** - critical photoperiod for diapause induction/termination.
  * **Adjustment rate for egg mortality** - adjustment rate for egg mortality.
  * **Adjustment rate for nymph mortality** - adjustment rate for nymph mortality.
@@ -77,7 +81,7 @@
  * **Adjustment of degree-days accumulation (egg->young nymph)** - adjustment of degree-days accumulation (egg->young nymph).
  * **Adjustment of degree-days accumulation (young nymph->old nymph)** - adjustment of degree-days accumulation (young nymph->old nymph).
  * **Adjustment of degree-days accumulation (old nymph->adult)** - adjustment of degree-days accumulation (old nymph->adult).
- * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
+ * **Plot standard error** - add standard error lines to plot.
 
     </help>
     <citations>