Mercurial > repos > tduigou > icfree_instructor

changeset 8:41755b74732c draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit b669b043a7cd633a9ba1ac2cf2a7f3ed09c3e92e-dirty
author tduigou
date Tue, 10 Sep 2024 14:54:30 +0000
parents 2571577e3b0c
children 25a9788e84ba
files instructor.xml test-data/instructor.hela.test-2.csv test-data/instructor.test-1.csv test-data/instructor.test-2.csv
diffstat 4 files changed, 24 insertions(+), 115 deletions(-) [+]
line wrap: on
line diff
--- a/instructor.xml	Tue Sep 10 14:24:36 2024 +0000
+++ b/instructor.xml	Tue Sep 10 14:54:30 2024 +0000
@@ -11,7 +11,8 @@
             '$destination_plate_file'
             'instructor.csv'
             --source_plate_type '$adv.source_plate_type'
-            --max_transfer_volume '$adv.max_transfer_volume'
+            #if str($adv.max_transfer_volume) != ''
+                --max_transfer_volume '$adv.max_transfer_volume'
             #if str($adv.split_threshold) != ''
                 --split_threshold '$adv.split_threshold'
             #end if
@@ -26,8 +27,8 @@
             <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="integer" min="3" 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="integer" min="3" 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>
--- a/test-data/instructor.hela.test-2.csv	Tue Sep 10 14:24:36 2024 +0000
+++ b/test-data/instructor.hela.test-2.csv	Tue Sep 10 14:54:30 2024 +0000
@@ -1,11 +1,7 @@
 Source Plate Name,Source Plate Type,Source Well,Destination Plate Name,Destination Well,Transfer Volume,Sample ID
 Source[1],384PP_AQ_CP,{A1;B1},Destination[1],A1,492.5,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],B1,500.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],B1,470.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],C1,500.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],C1,37.5,Hela lysate
+Source[1],384PP_AQ_CP,{A1;B1},Destination[1],B1,970.0,Hela lysate
+Source[1],384PP_AQ_CP,{A1;B1},Destination[1],C1,537.5,Hela lysate
 Source[1],384PP_AQ_CP,{A1;B1},Destination[1],D1,492.5,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],E1,500.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],E1,470.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],F1,500.0,Hela lysate
-Source[1],384PP_AQ_CP,{A1;B1},Destination[1],F1,37.5,Hela lysate
+Source[1],384PP_AQ_CP,{A1;B1},Destination[1],E1,970.0,Hela lysate
+Source[1],384PP_AQ_CP,{A1;B1},Destination[1],F1,537.5,Hela lysate
--- a/test-data/instructor.test-1.csv	Tue Sep 10 14:24:36 2024 +0000
+++ b/test-data/instructor.test-1.csv	Tue Sep 10 14:54:30 2024 +0000
@@ -6,15 +6,11 @@
 Source[1],384PP_AQ_GP3,C1,Destination[1],E1,165.0,Access prot 50%
 Source[1],384PP_AQ_GP3,C1,Destination[1],F1,325.0,Access prot 50%
 Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],A1,492.5,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],B1,500.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],B1,470.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],C1,500.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],C1,37.5,Hela lysate
+Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],B1,970.0,Hela lysate
+Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],C1,537.5,Hela lysate
 Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],D1,492.5,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],E1,500.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],E1,470.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],F1,500.0,Hela lysate
-Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],F1,37.5,Hela lysate
+Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],E1,970.0,Hela lysate
+Source[1],384PP_AQ_GP3,{A1;B1},Destination[1],F1,537.5,Hela lysate
 Source[1],384PP_AQ_GP3,E1,Destination[1],A1,152.5,RNA 1ug/uL
 Source[1],384PP_AQ_GP3,E1,Destination[1],B1,112.5,RNA 1ug/uL
 Source[1],384PP_AQ_GP3,E1,Destination[1],C1,185.0,RNA 1ug/uL
@@ -27,51 +23,9 @@
 Source[1],384PP_AQ_GP3,D1,Destination[1],D1,310.0,Reaction mix
 Source[1],384PP_AQ_GP3,D1,Destination[1],E1,257.5,Reaction mix
 Source[1],384PP_AQ_GP3,D1,Destination[1],F1,192.5,Reaction mix
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,20.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,495.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,260.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,20.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,495.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,260.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],A1,4020.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],B1,3495.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],C1,3760.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],D1,4020.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],E1,3495.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],F1,3760.0,Water
--- a/test-data/instructor.test-2.csv	Tue Sep 10 14:24:36 2024 +0000
+++ b/test-data/instructor.test-2.csv	Tue Sep 10 14:54:30 2024 +0000
@@ -17,51 +17,9 @@
 Source[1],384PP_AQ_GP3,D1,Destination[1],D1,310.0,Reaction mix
 Source[1],384PP_AQ_GP3,D1,Destination[1],E1,257.5,Reaction mix
 Source[1],384PP_AQ_GP3,D1,Destination[1],F1,192.5,Reaction mix
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],A1,20.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],B1,495.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],C1,260.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],D1,20.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],E1,495.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,500.0,Water
-Source[1],384PP_AQ_GP3,F1,Destination[1],F1,260.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],A1,4020.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],B1,3495.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],C1,3760.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],D1,4020.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],E1,3495.0,Water
+Source[1],384PP_AQ_GP3,F1,Destination[1],F1,3760.0,Water