# HG changeset patch
# User greg
# Date 1519756309 18000
# Node ID d9371485aaf519244c5ced8b00d69c05fd4c2889
# Parent  37f1ad91a94947060a287e07882962d7afd07e5a
Uploaded

diff -r 37f1ad91a949 -r d9371485aaf5 insect_phenology_model.xml
--- a/insect_phenology_model.xml	Tue Feb 13 13:53:37 2018 -0500
+++ b/insect_phenology_model.xml	Tue Feb 27 13:31:49 2018 -0500
@@ -4,6 +4,20 @@
         <requirement type="package" version="1.4.4">r-optparse</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+#set stages = list()
+#set life_stages_adult = "None"
+#set life_stage_nymph = "None"
+#set life_stages = $life_stages_cond.life_stages
+#for life_stage in str($life_stages).split(","):
+    #if $life_stage == "Adult":
+        #set life_stages_adult = $life_stages_cond.life_stages_adult
+    #else if $life_stage == "Nymph":
+        #set life_stage_nymph = $life_stages_cond.life_stage_nymph
+    #end if
+    $stages.append($life_stage)
+#end for
+#set stages = ",".join($stages)
+mkdir output_dir &&
 Rscript '$__tool_directory__/insect_phenology_model.R'
 --adult_mortality $adult_mortality
 --adult_accumulation $adult_accumulation
@@ -11,25 +25,32 @@
 --input '$input'
 --insect '$insect'
 --insects_per_replication $insects_per_replication
+--life_stages '$stages'
+#if str($life_stages_adult) != "None":
+    --life_stages_adult $life_stages_adult
+#end if
+#if str($life_stage_nymph) != "None":
+    --life_stage_nymph $life_stage_nymph
+#end if
 --location '$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
+--plot_generations_separately $plot_generations_separately
+--plot_std_error $plot_std_error
 --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" />
         <param name="insect" type="select" label="Select insect">
-            <option value="Brown Marmorated Stink Bug" selected="True">Brown Marmorated Stink Bug</option>
+            <option value="BMSB" selected="True">Brown Marmorated Stink Bug</option>
         </param>
-        <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
+        <param name="replications" type="integer" value="10" min="2" 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" />
@@ -41,20 +62,53 @@
         <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 name="plot_generations_separately" type="select" label="Plot generations separately?">
+            <option value="yes" selected="True">Yes</option>
+            <option value="no">No</option>
+        </param>
+        <conditional name="life_stages_cond" label="Select life_stages for plotting">
+            <param name="life_stages" type="select" label="Select life stages for plotting">
+                <option value="Total" selected="true">All</option>
+                <option value="Egg">Egg</option>
+                <option value="Nymph">Nymph</option>
+                <option value="Adult">Adult</option>
+            </param>
+            <when value="Total"/>
+            <when value="Egg"/>
+            <when value="Nymph">
+                <param name="life_stage_nymph" type="select" label="Select nymph life stage">
+                    <option value="Total" selected="true">All</option>
+                    <option value="Young">Young</option>
+                    <option value="Old">Old</option>
+                </param>
+            </when>
+            <when value="Adult">
+                <param name="life_stages_adult" type="select" label="Select adult life stage">
+                    <option value="Total" selected="true">All</option>
+                    <option value="Pre-vittelogenic">Pre-vittelogenic</option>
+                    <option value="Vittelogenic">Vittelogenic</option>
+                    <option value="Diapausing">Diapausing</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="plot_std_error" type="select" label="Plot standard error?">
+            <option value="yes" selected="True">Yes</option>
+            <option value="no">No</option>
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="pdf" label="${tool.name} ${location}, on ${on_string}" />
+        <collection name="output_collection" type="list" label="${tool.name} ${location}, on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output_dir" format="pdf" />
+        </collection>
     </outputs>
     <tests>
         <test>
             <param name="input" value="state_college.csv" ftype="csv" />
             <param name="location" value="State College PA" />
             <param name="replications" value="10" />
-            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+            <output_collection name="output_collection" type="list">
+                <element name="output.pdf" file="output.pdf" ftype="pdf" compare="contains"/>
+            </output_collection>
         </test>
     </tests>
     <help>
@@ -81,6 +135,8 @@
  * **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 generations separately** - select "Yes" to plot P, F1 and F2 as separate lines or "no" to pool across generations, resulting in a total for the selected life states.
+ * **Select life stages for plotting** - select any combinaton of Egg, Nymph, Adult or "All" for plotting.
  * **Plot standard error** - add standard error lines to plot.
 
     </help>