tests(tools): icfree, update test

brsynth · Jul 5, 2024 · 8b53f1a · 8b53f1a
1 parent 1cd33b3
commit 8b53f1a
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diff --git a/tools/icfree/instructor.xml b/tools/icfree/instructor.xml
@@ -9,7 +9,7 @@
         python icfree/instructor.py
             '$source_plate_file'
             '$destination_plate_file'
-            'Instruction'
+            'instructor.csv'
             --source_plate_type '$source_plate_type'
             --max_transfer_volume '$max_transfer_volume'
             --split_threshold '$split_threshold'
@@ -28,10 +28,32 @@
         </section>
     </inputs>
     <outputs>
-        <data name="output_instruction" format="list" label="${tool.name} - Instructor">
+        <data name="output_instructor" format="list" label="${tool.name} - Instructor">
             <discover_datasets pattern="__designation_and_ext__" format="csv" />
         </data>
     </outputs>
+    <tests>
+        <test>
+            <!-- python -m icfree.instructor source_plate.csv destination_plate.csv Instruction.csv -->
+            <param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" />
+            <param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" />
+            <output_collection name="output_instructor" type="list" count="1">
+                <element name="instructor.csv" file="instructor.test-1.csv" ftype="tabular" compare="diff" />
+            </output_collection>
+        </test>
+        <test>
+            <!-- python -m icfree.instructor source_plate.csv destination_plate.csv Instruction.csv --source_plate_type "Hela lysate:384PP_AQ_CP,Access prot 50%:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3" --split_components "Hela lysate,Access prot 50%" -->
+            <param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" />
+            <param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" />
+            <param name="source_plate_type" value="Hela lysate:384PP_AQ_CP,Access prot 50%:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3" />
+            <param name="split_components" value="Hela lysate,Access prot 50%" />
+            <output_collection name="output_instructor" type="list" count="2">
+                <element name="instructor.csv" file="instructor.test-2.csv" ftype="tabular" compare="diff" />
+                <element name="instructor_Hela lysate.csv" file="instructor.hela.test-2.csv" ftype="tabular" compare="diff" />
+                <element name="instructor_Access prot 50%.csv" file="instructor.access.test-2.csv" ftype="tabular" compare="diff" />
+            </output_collection>
+        </test>
+    </tests>
     <help><![CDATA[
 Instructor
 ==========

diff --git a/tools/icfree/plates_designer.xml b/tools/icfree/plates_designer.xml
@@ -12,10 +12,10 @@
             #silent well_capacity.append(str($x.component_name) + "=" + str($x.well_capacity))
             #silent dead_volumes.append(str($x.component_name) + "=" + str($x.dead_volumes))
         #end for
-        #set swell_capacity = ','.join($well_capacity)
-        #set sdead_volumes = ','.join($dead_volumes)
+        #set swell_capacity = '"' + ','.join($well_capacity) + '"'
+        #set sdead_volumes = '"' + ','.join($dead_volumes) + '"'
 
-        python icfree/plates_designer.py
+        python -m icfree.plate_designer
             '$sampling_file'
             '$sample_volume'
             --start_well_src_plt '$adv.start_well_src_plt'
@@ -57,15 +57,57 @@
                 <param name="component_name" type="text" value="" label="Component Name">
                     <validator type="empty_field" message="Not empty"/>
                 </param>
-                <param name="well_capacity" type="integer" optional="60000" label="Well capacity" />
-                <param name="dead_volumes" type="integer" optional="15000" label="Dead volumes" />
+                <param name="well_capacity" type="integer" value="60000" label="Well capacity" />
+                <param name="dead_volumes" type="integer" value="15000" label="Dead volumes" />
             </repeat>
         </section>
     </inputs>
     <outputs>
         <data name="output_source_plate" format="tabular" label="${tool.name} - Source" />
         <data name="output_destination_plate" format="tabular" label="${tool.name} - Destination" />
     </outputs>
+    <tests>
+        <test>
+            <!-- python -m icfree.plate_designer sampling.test-1.tsv 6000 --default_well_capacity 60000 --default_dead_volume 20000 --num_replicates 1 -->
+            <param name="sampling_file" value="sampling.test-1.test" />
+            <param name="sample_volume" value="6000" />
+            <param name="default_well_capacity" value="60000" />
+            <param name="default_dead_volume" value="20000" />
+            <param name="num_replicates" value="1" />
+            <output name="output_source_plate" file="plates_generator.source_plate.test-1.tsv" ftype="tabular" compare="diff" />
+            <output name="output_destination_plate" file="plates_generator.source_plate.test-1.tsv" ftype="tabular" compare="diff" />
+        </test>
+        <test>
+            <!-- python -m icfree.plate_designer sampling.test-1.tsv 5000 --default_well_capacity 60000 --default_dead_volume 20000 --num_replicates 2 --well_capacity "Hela lysate=3000,Access prot 50%=4000,Reaction mix=3000,RNA 1ug/uL=2000" --dead_volumes "Hela lysate=30,Access prot 50%=5,Reaction mix=10,RNA 1ug/uL=20" -->
+            <param name="sampling_file" value="sampling.test-1.test" />
+            <param name="sample_volume" value="5000" />
+            <param name="default_well_capacity" value="60000" />
+            <param name="default_dead_volume" value="20000" />
+            <param name="num_replicates" value="2" />
+            <repeat name="rep">
+                <param name="component_name" value="Hela lysate" />
+                <param name="well_capacity" value="3000" />
+                <param name="dead_volumes" value="30" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="Access prot 50%" />
+                <param name="well_capacity" value="4000" />
+                <param name="dead_volumes" value="5" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="Reaction mix" />
+                <param name="well_capacity" value="3000" />
+                <param name="dead_volumes" value="10" />
+            </repeat>
+            <repeat name="rep">
+                <param name="component_name" value="RNA 1ug/uL" />
+                <param name="well_capacity" value="2000" />
+                <param name="dead_volumes" value="20" />
+            </repeat>
+            <output name="output_source_plate" file="plates_generator.source_plate.test-2.tsv" ftype="tabular" compare="diff" />
+            <output name="output_destination_plate" file="plates_generator.source_plate.test-2.tsv" ftype="tabular" compare="diff" />
+        </test>
+    </tests>
     <help><![CDATA[
 Plates Generator
 ================

diff --git a/tools/icfree/test-data/converter_proCFPS_parameters.tsv b/tools/icfree/test-data/converter_proCFPS_parameters.tsv
diff --git a/tools/icfree/test-data/converter_sampling_concentrations.tsv b/tools/icfree/test-data/converter_sampling_concentrations.tsv