--- a/instructor.xml	Tue Sep 10 13:17:59 2024 +0000
+++ b/instructor.xml	Wed Nov 13 12:55:41 2024 +0000
@@ -4,14 +4,16 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
     <command detect_errors="exit_code"><![CDATA[
+        mkdir -p outdir &&
         python -m icfree.instructor
             '$source_plate_file'
             '$destination_plate_file'
-            'instructor.csv'
+            'outdir/instructions.csv'
             --source_plate_type '$adv.source_plate_type'
-            --max_transfer_volume '$adv.max_transfer_volume'
+            #if str($adv.max_transfer_volume) != ''
+                --max_transfer_volume '$adv.max_transfer_volume'
+            #end if
             #if str($adv.split_threshold) != ''
                 --split_threshold '$adv.split_threshold'
             #end if
@@ -26,15 +28,15 @@
             <param name="source_plate_type" type="text" value="default:384PP_AQ_GP3" label="Source plate type" help="Comma-separated list of component and plate type pairs, e.g., 'Component_1:384PP_AQ_CP,Component_2:384PP_AQ_GP3'. Default for all is default:384PP_AQ_GP3." >
                 <validator type="empty_field" message="Source plate type is required"/>
             </param>
-            <param argument="max_transfer_volume" type="float" min="2.5" max="500000" value="100000" label="Maximum transfer volume" help="Maximum volume for a single transfer. If not specified, no splitting will be performed." />
-            <param argument="split_threshold" type="float" min="2.5" max="500000" value="100000" label="Split threshold" help="Volume threshold above which transfers need to be split. If not specified, no splitting will be performed." />
+            <param argument="max_transfer_volume" type="integer" optional="true" label="Maximum transfer volume" help="Maximum volume for a single transfer. If not specified, no splitting will be performed." />
+            <param argument="split_threshold" type="integer" optional="true" label="Split threshold" help="Volume threshold above which transfers need to be split. If not specified, no splitting will be performed." />
             <param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." >
             </param>
         </section>
     </inputs>
     <outputs>
-        <collection name="output_instructor" type="list" label="${tool.name} - Instructor">
-            <discover_datasets pattern="__designation_and_ext__" format="csv" directory="."/>
+        <collection name="output_instructor" type="list" label="${tool.name} - Instructions">
+            <discover_datasets pattern="__designation_and_ext__" format="csv" directory="outdir"/>
         </collection>
     </outputs>
     <tests>
@@ -43,7 +45,7 @@
             <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
             <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
             <output_collection name="output_instructor" type="list" count="1">
-                <element name="instructor" file="instructor.test-1.csv" ftype="csv" compare="diff" />
+                <element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" />
             </output_collection>
         </test>
         <test>
@@ -53,8 +55,8 @@
             <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="3">
-                <element name="instructor" file="instructor.test-2.csv" ftype="csv" compare="diff" />
-                <element name="instructor_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />
+                <element name="instructions" file="instructor.test-2.csv" ftype="csv" compare="diff" />
+                <element name="instructions_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />
                 <!--
                     <element name="instructor_Access prot 50X" file="instructor.access.test-2.csv" ftype="csv" compare="diff" />
                 -->