diff extract_ipm_date_interval.xml @ 10:c2eb16ef23c0 draft

Uploaded

--- a/extract_ipm_date_interval.xml	Wed Aug 01 09:18:55 2018 -0400
+++ b/extract_ipm_date_interval.xml	Tue Aug 07 13:02:58 2018 -0400
@@ -1,89 +1,85 @@
 <tool id="ipm_date_interval" name="Extract date interval" version="1.1.0">
     <description>from insect phenology model data</description>
     <requirements>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+        <requirement type="package" version="2.2.6">r-hash</requirement>
         <requirement type="package" version="1.4.4">r-optparse</requirement>
-        <requirement type="package" version="1.10.4">r-data.table</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#set input_dir = 'input_dir'
+#set input_data_dir = 'input_data_dir'
 #set output_data_dir = "output_data_dir"
 #set output_plots_dir = "output_plots_dir"
 #set error_file = $os.path.join($output_data_dir, "04_combined_generations.csv")
-mkdir $input_dir &&
+#set job = $input_data[0].creating_job
+#set tool_parameters = ""
+#for $p in $job.parameters:
+    #set tool_parameters = $tool_parameters + "__SeP__" + $p.name
+    #set tool_parameters = $tool_parameters + "__SeP__" + $p.value
+#end for
+mkdir $input_data_dir &&
 mkdir output_data_dir &&
 mkdir output_plots_dir &&
-#for $i in $input:
+#for $i in $input_data:
     #set filename = $i.file_name
     #set name = $i.name
-    ln -s $filename $input_dir/$name &&
+    ln -s $filename $input_data_dir/$name &&
 #end for
 Rscript '$__tool_directory__/extract_ipm_date_interval.R'
 --end_date '$end_date'
---input_dir '$input_dir'
---plot_std_error $plot_std_error
+--input_data_dir '$input_data_dir'
 --script_dir '$__tool_directory__'
 --start_date '$start_date'
-&>ipm_log.txt;
+--tool_parameters '$tool_parameters'
+&>eipmdi_log.txt;
 if [[ $? -ne 0 ]]; then
-    cp ipm_log.txt '$error_file';
+    cp eipmdi_log.txt '$error_file';
     exit 1;
 fi]]></command>
     <inputs>
-        <param name="input" type="data_collection" format="csv" collection_type="list" label="Insect phenology model data files" />
+        <param name="input_data" type="data_collection" format="csv" collection_type="list" label="Insect phenology model data files" />
         <param name="start_date" type="text" value="" label="Start date" help="Format must be yyyy-mm-dd">
             <validator type="expression" message="Date must have the format yyyy-mm-dd">len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2])</validator>
         </param>
         <param name="end_date" type="text" value="" label="End date" help="Format must be yyyy-mm-dd">
             <validator type="expression" message="Date must have the format yyyy-mm-dd">len(value.split('-')[0])==4 and int(value.split('-')[0]) and len(value.split('-')[1])==2 and int(value.split('-')[1]) and len(value.split('-')[2])==2 and int(value.split('-')[2])</validator>
         </param>
-        <param name="plot_std_error" type="select" label="Plot standard error?">
-            <option value="yes" selected="True">Yes</option>
-            <option value="no">No</option>
-        </param>
     </inputs>
     <outputs>
         <collection name="output_data_collection" type="list" label="${tool.name} (data), on ${on_string}">
             <discover_datasets pattern="__name__" directory="output_data_dir" format="csv"/>
         </collection>
-        <collection name="output_plots_collection" type="list" label="${tool.name} (plots), on ${on_string}">
+        <collection name="output_plot_collection" type="list" label="${tool.name} (plots), on ${on_string}">
             <discover_datasets pattern="__name__" directory="output_plots_dir" format="pdf"/>
         </collection>
     </outputs>
     <tests>
         <test>
-            <param name="input">
+            <!--
+            FIXME: Here is a sort of layout for a test, but since the input collection will be uploaded, the test
+            will fail bacused the job parameters for the inputs will not be those produced by the insect_phenology_model
+            tool.  Testing this tool will require using the workflow testing approach.
+            <param name="input_data">
                 <collection type="list">
-                    <element name="04_combined_generations.csv"/>
+                    <element name="input_p_1.csv" value="input_p_1.csv" ftype="csv"/>
+                    <element name="input_f1_1.csv" value="input_f1_1.csv" ftype="csv"/>
+                    <element name="input_f2_1.csv" value="input_f2_1.csv" ftype="csv"/>
+                    <element name="input_combined1.csv" value="input_combined1.csv" ftype="csv"/>
                 </collection>
             </param>
             <param name="start_date" value="2017-04-01"/>
             <param name="end_date" value="2017-04-15"/>
             <output_collection name="output_data_collection" type="list">
-                <element name="04_combined_generations.csv" file="output_combined6.csv" ftype="csv" compare="contains"/>
-            </output_collection>
-            <!--
-            <output_collection name="output_plots_collection" type="list">
-                <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
-                <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="01_generation_P.csv" file="output_p_1.csv" ftype="csv" compare="contains"/>
+                <element name="02_generation_F1.csv" file="output_f1_1.csv" ftype="csv" compare="contains"/>
+                <element name="03_generation_F2.csv" file="output_f2_1.csv" ftype="csv" compare="contains"/>
+                <element name="04_combined_generations.csv" file="output_combined1.csv" ftype="csv" compare="contains"/>
             </output_collection>
-            -->
-        </test>
-        <test>
-            <param name="input">
-                <collection type="list">
-                    <element name="04_combined_generations.csv"/>
-                </collection>
-            </param>
-            <param name="start_date" value="2017-01-01"/>
-            <param name="end_date" value="2017-01-15"/>
-            <output_collection name="output_data_collection" type="list">
-                <element name="04_combined_generations.csv" file="output_combined7.csv" ftype="csv" compare="contains"/>
-            </output_collection>
-            <!--
-            <output_collection name="output_plots_collection" type="list">
-                <element name="02_young_nymph_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
-                <element name="05_pre-vittelogenic_adult_pop.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+            <output_collection name="output_plot_collection" type="list">
+                <element name="01_egg_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="04_total_nymph_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="08_total_adult_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
+                <element name="09_total_pop_by_generation.pdf" file="plot.pdf" ftype="pdf" compare="contains"/>
             </output_collection>
             -->
         </test>