--- a/insect_phenology_model.xml	Wed Nov 22 13:22:49 2017 -0500
+++ b/insect_phenology_model.xml	Wed Dec 06 10:07:21 2017 -0500
@@ -5,23 +5,24 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/insect_phenology_model.R'
--a $adult_mort
--b $adult_accum
--c $egg_mort
--e '$location'
--f $max_clutch_size
--i $min_clutch_size
--j $nymph_mort
--k $old_nymph_accum
--n $input.metadata.data_lines
--o '$output'
--p $oviposition
--q $photoperiod
--s $replications
--t $se_plot
--v '$input'
--y $young_nymph_accum
--x '$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" />
@@ -29,17 +30,18 @@
             <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_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
-        <param name="nymph_mort" type="integer" value="1" min="0" label="Adjustment rate for nymph mortality" />
-        <param name="adult_mort" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
+        <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" />
+        <param name="adult_mortality" type="integer" value="1" min="0" label="Adjustment rate for adult mortality" />
         <param name="oviposition" type="integer" value="1" min="0" label="Adjustment oviposition rate" />
         <param name="min_clutch_size" type="integer" value="0" min="0" label="Adjustment of minimum clutch size" />
         <param name="max_clutch_size" type="integer" value="0" min="0" label="Adjustment of maximum clutch size" />
-        <param name="young_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (egg->young nymph)" />
-        <param name="old_nymph_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (young nymph->old nymph)" />
-        <param name="adult_accum" type="integer" value="0" min="0" label="Adjustment of DD accumulation (old nymph->adult)" />
-        <param name="se_plot" type="select" label="Plot SE?">
+        <param name="young_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (egg->young nymph)" />
+        <param name="old_nymph_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (young nymph->old nymph)" />
+        <param name="adult_accumulation" type="integer" value="0" min="0" label="Adjustment of degree-days accumulation (old nymph->adult)" />
+        <param name="std_error_plot" type="select" label="Plot standard error?">
             <option value="1" selected="True">Yes</option>
             <option value="0">No</option>
         </param>
@@ -57,7 +59,7 @@
     </tests>
     <help>
 **What it does**
- 
+
 Provides an agent-based stochastic model expressing stage-specific phenology and population dynamics for an insect species across geographic regions.
 
 -----
@@ -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.
@@ -74,11 +78,11 @@
  * **Adjustment oviposition rate** - adjustment oviposition rate.
  * **Adjustment of minimum clutch size** - adjustment of minimum clutch size.
  * **Adjustment of maximum clutch size** - adjustment of maximum clutch size
- * **Adjustment of DD accumulation (egg->young nymph)** - adjustment of DD accumulation (egg->young nymph).
- * **Adjustment of DD accumulation (young nymph->old nymph)** - adjustment of DD accumulation (young nymph->old nymph).
- * **Adjustment of DD accumulation (old nymph->adult)** - adjustment of DD accumulation (old nymph->adult).
- * **Plot SE** - add SE lines to plot for eggs, nymphs and adults.
- 
+ * **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 standard error** - add standard error lines to plot.
+
     </help>
     <citations>
         <citation type="doi">10.3389/fphys.2016.00165</citation>