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comparison instructor.xml @ 24:5714db441be6 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit b09df1450c87c2254b7a3ffddc3ed16208a3ab50
author tduigou
date Fri, 07 Feb 2025 11:07:06 +0000
parents a97e39607eab
children 20b09754089b
comparison
equal deleted inserted replaced
23:923a2cf98a30 24:5714db441be6
18 --split_threshold '$adv.split_threshold' 18 --split_threshold '$adv.split_threshold'
19 #end if 19 #end if
20 #if str($adv.split_components) != '' 20 #if str($adv.split_components) != ''
21 --split_components '$adv.split_components' 21 --split_components '$adv.split_components'
22 #end if 22 #end if
23 #if str($adv.dispense_order) != ''
24 --dispense_order '$adv.dispense_order'
25 #end if
26 ]]></command> 23 ]]></command>
27 <inputs> 24 <inputs>
28 <param name="source_plate_file" type="data" format="csv" label="Source corresponding to plate/wells" help="Output from iCFree plates designer"/> 25 <param name="source_plate_file" type="data" format="csv" label="Source corresponding to plate/wells" help="Output from iCFree plates designer"/>
29 <param name="destination_plate_file" type="data" format="csv" label="Destination corresponding to plate/wells" help="Output from iCFree plates designer"/> 26 <param name="destination_plate_file" type="data" format="csv" label="Destination corresponding to plate/wells" help="Output from iCFree plates designer"/>
30 <section name="adv" title="Advanced Options" expanded="false"> 27 <section name="adv" title="Advanced Options" expanded="false">
31 <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." > 28 <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." >
32 <validator type="empty_field" message="Source plate type is required"/> 29 <validator type="empty_field" message="Source plate type is required"/>
33 </param> 30 </param>
34 <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." /> 31 <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." />
35 <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." /> 32 <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." />
36 <param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." /> 33 <param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." >
37 <param name="dispense_order" type="text" optional="true" label="Dispense order" help="Comma-separated list of component specifying dispensing order." /> 34 </param>
38 </section> 35 </section>
39 </inputs> 36 </inputs>
40 <outputs> 37 <outputs>
41 <collection name="output_instructor" type="list" label="${tool.name} - Instructions"> 38 <collection name="output_instructor" type="list" label="${tool.name} - Instructions">
42 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="outdir"/> 39 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="outdir"/>
43 </collection> 40 </collection>
44 </outputs> 41 </outputs>
45 <tests> 42 <tests>
46 <test> 43 <test>
47 <!-- python -m icfree.instructor ../plate_designer.source_plate.test-2.csv ../plate_designer.destination_plate.test-2.csv 'instructor.test-1.csv' -source_plate_type 'default:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' --> 44 <!-- python -m icfree.instructor plates_designer.source_plate.test-2.csv plates_designer.destination_plate.test-2.csv 'instructor.test-1.csv' -source_plate_type 'default:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -->
48 <param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" /> 45 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
49 <param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" /> 46 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
50 <param name="max_transfer_volume" value="500" />
51 <param name="split_threshold" value="500" />
52 <output_collection name="output_instructor" type="list" count="1"> 47 <output_collection name="output_instructor" type="list" count="1">
53 <element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" /> 48 <element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" />
54 </output_collection> 49 </output_collection>
55 </test> 50 </test>
56 <test> 51 <test>
57 <!-- python -m icfree.instructor plate_designer.source_plate.test-2.csv plate_designer.destination_plate.test-2.csv 'instructor.csv' -source_plate_type 'Hela lysate:384PP_AQ_CP,Access prot 50X:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -split_components 'Hela lysate,Access prot 50X' -dispense_order 'Access prot 50X,Hela lysate' --> 52 <!-- python -m icfree.instructor plates_designer.source_plate.test-2.csv plates_designer.destination_plate.test-2.csv 'instructor.csv' -source_plate_type 'Hela lysate:384PP_AQ_CP,Access prot 50X:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3' -max_transfer_volume '500' -split_threshold '500' -split_components 'Hela lysate,Access prot 50X' -->
58 <param name="source_plate_file" value="plate_designer.source_plate.test-2.csv" /> 53 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
59 <param name="destination_plate_file" value="plate_designer.destination_plate.test-2.csv" /> 54 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
60 <param name="max_transfer_volume" value="500" />
61 <param name="split_threshold" value="500" />
62 <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" /> 55 <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" />
63 <param name="split_components" value="Hela lysate,Access prot 50%" /> 56 <param name="split_components" value="Hela lysate,Access prot 50%" />
64 <output_collection name="output_instructor" type="list" count="3"> 57 <output_collection name="output_instructor" type="list" count="3">
65 <element name="instructions" file="instructor.test-2.csv" ftype="csv" compare="diff" /> 58 <element name="instructions" file="instructor.test-2.csv" ftype="csv" compare="diff" />
66 <element name="instructions_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" /> 59 <element name="instructions_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />