changeset 2:07444af6824f draft

Uploaded

--- a/insect_phenology_model.xml	Wed Aug 09 07:32:42 2017 -0400
+++ b/insect_phenology_model.xml	Mon Aug 14 13:47:50 2017 -0400
@@ -2,23 +2,20 @@
 <tool id="insect_phenology_model" name="Insect phenology model" version="1.0.0">
     <description>expressing stage-specific phenology and population dynamics</description>
     <requirements>
-         <requirement type="package" version="1.3.0">r-optparse</requirement>
+         <requirement type="package" version="1.3.2">r-optparse</requirement>
     </requirements>
-    <command><![CDATA[
-#set loc_lat_items = str($location).split(':')
-#set loc = $loc_lat_items[0]
-#set lat = $loc_lat_items[1]
+    <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/insect_phenology_model.R'
 -a $adult_mort
 -b $adult_accum
 -c $egg_mort
--d $lat
--e $loc
+-d $latitude
+-e '$location'
 -f $max_clutch_size
 -i $min_clutch_size
 -j $nymph_mort
 -k $old_nymph_accum
--o $output
+-o '$output'
 -p $oviposition
 -q $photoperiod
 -s $replications
@@ -28,19 +25,10 @@
 -y $young_nymph_accum
     ]]></command>
     <inputs>
-        <param name="location" type="select" label="Location">
-            <options from_file="locations.txt">
-                <column name="name" index="0"/>
-                <column name="value" index="1"/>
-            </options>
-        </param>
+        <param name="location" type="text" value="" optional="false" label="Location" />
+        <param name="latitude" type="float" value="0.0" label="Latitude of selected location" />
         <param name="temperature_data" type="data" format="csv" label="Temperature data" />
-        <param name="year" type="select" label="Temperature data year">
-            <options from_file="years.txt">
-                <column name="name" index="0"/>
-                <column name="value" index="1"/>
-            </options>
-        </param>
+        <param name="year" type="integer" value="2017" min="1995" label="Temperature data year" />
         <param name="replications" type="integer" value="10" min="1" label="Number of replications" />
         <param name="photoperiod" type="float" value="13.5" min="0" label="Critical photoperiod for diapause induction/termination" />
         <param name="egg_mort" type="integer" value="1" min="0" label="Adjustment rate for egg mortality" />
@@ -58,7 +46,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="output" format="pdf" label="${tool.name} ${str($location).split(':')[0]}, ${year} on ${on_string}" />
+        <data name="output" format="pdf" label="${tool.name} ${location}, ${year} lat:${latitude} on ${on_string}" />
     </outputs>
     <tests>
         <test>