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comparison instructor.xml @ 24:2e83e43e004b draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit d82c78285bc6ce4bb318fc8d3fa353e8c6135135-dirty
author tduigou
date Wed, 13 Nov 2024 12:55:41 +0000
parents 5ba334474596
children
comparison
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23:7ddf9e4b39db 24:2e83e43e004b
2 <description>Generates a list of Echo-compatible instructions to prepare samples</description> 2 <description>Generates a list of Echo-compatible instructions to prepare samples</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir -p outdir &&
9 python -m icfree.instructor 9 python -m icfree.instructor
10 '$source_plate_file' 10 '$source_plate_file'
11 '$destination_plate_file' 11 '$destination_plate_file'
12 'instructor.csv' 12 'outdir/instructions.csv'
13 --source_plate_type '$adv.source_plate_type' 13 --source_plate_type '$adv.source_plate_type'
14 --max_transfer_volume '$adv.max_transfer_volume' 14 #if str($adv.max_transfer_volume) != ''
15 --max_transfer_volume '$adv.max_transfer_volume'
16 #end if
15 #if str($adv.split_threshold) != '' 17 #if str($adv.split_threshold) != ''
16 --split_threshold '$adv.split_threshold' 18 --split_threshold '$adv.split_threshold'
17 #end if 19 #end if
18 #if str($adv.split_components) != '' 20 #if str($adv.split_components) != ''
19 --split_components '$adv.split_components' 21 --split_components '$adv.split_components'
24 <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"/>
25 <section name="adv" title="Advanced Options" expanded="false"> 27 <section name="adv" title="Advanced Options" expanded="false">
26 <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." >
27 <validator type="empty_field" message="Source plate type is required"/> 29 <validator type="empty_field" message="Source plate type is required"/>
28 </param> 30 </param>
29 <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." /> 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." />
30 <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." /> 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." />
31 <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." >
32 </param> 34 </param>
33 </section> 35 </section>
34 </inputs> 36 </inputs>
35 <outputs> 37 <outputs>
36 <collection name="output_instructor" type="list" label="${tool.name} - Instructor"> 38 <collection name="output_instructor" type="list" label="${tool.name} - Instructions">
37 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="."/> 39 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="outdir"/>
38 </collection> 40 </collection>
39 </outputs> 41 </outputs>
40 <tests> 42 <tests>
41 <test> 43 <test>
42 <!-- 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' --> 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' -->
43 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" /> 45 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
44 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" /> 46 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
45 <output_collection name="output_instructor" type="list" count="1"> 47 <output_collection name="output_instructor" type="list" count="1">
46 <element name="instructor" file="instructor.test-1.csv" ftype="csv" compare="diff" /> 48 <element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" />
47 </output_collection> 49 </output_collection>
48 </test> 50 </test>
49 <test> 51 <test>
50 <!-- 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' --> 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' -->
51 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" /> 53 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
52 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" /> 54 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
53 <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" />
54 <param name="split_components" value="Hela lysate,Access prot 50%" /> 56 <param name="split_components" value="Hela lysate,Access prot 50%" />
55 <output_collection name="output_instructor" type="list" count="3"> 57 <output_collection name="output_instructor" type="list" count="3">
56 <element name="instructor" file="instructor.test-2.csv" ftype="csv" compare="diff" /> 58 <element name="instructions" file="instructor.test-2.csv" ftype="csv" compare="diff" />
57 <element name="instructor_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" />
58 <!-- 60 <!--
59 <element name="instructor_Access prot 50X" file="instructor.access.test-2.csv" ftype="csv" compare="diff" /> 61 <element name="instructor_Access prot 50X" file="instructor.access.test-2.csv" ftype="csv" compare="diff" />
60 --> 62 -->
61 </output_collection> 63 </output_collection>
62 </test> 64 </test>