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* feat(tools): icfree-ml, update to * tests(tools): icfree, rm tests * tests(tools): icfree, update test * feat(tools): icfree, update to 2.4.0 * feat(tools): icfree, update to 2.4.0 * fix(tools): icfree, mv test files * fix(tools): icfree, mv test files * fix(tools): icfree, misc * fix(tools): icfree, mv plates_designer constrained by toolshed * fix(tools): icfree, mv plates_generator to plates_designer
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| <tool id="icfree_plates_designer" name="iCFree plates designer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT"> | ||
| <description>Prepare source and destination well-plate mappings with advanced options.</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <expand macro="stdio"/> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| #set well_capacity = [] | ||
| #set dead_volumes = [] | ||
| #for $x in $adv.rep | ||
| #silent well_capacity.append(str($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($dead_volumes) | ||
| python -m icfree.plate_designer | ||
| '$sampling_file' | ||
| '$sample_volume' | ||
| --start_well_src_plt '$adv.start_well_src_plt' | ||
| --start_well_dst_plt '$adv.start_well_dst_plt' | ||
| --plate_dims '$adv.plate_dims' | ||
| #if len($well_capacity) > 0 | ||
| --well_capacity '$swell_capacity' | ||
| #end if | ||
| --default_well_capacity '$adv.default_well_capacity' | ||
| #if len($dead_volumes) > 0 | ||
| --dead_volumes '$sdead_volumes' | ||
| #end if | ||
| --default_dead_volume '$adv.default_dead_volume' | ||
| --num_replicates '$adv.num_replicates' && | ||
| mv source_plate.csv '$output_source_plate' && | ||
| mv destination_plate.csv '$output_destination_plate' | ||
| ]]></command> | ||
| <inputs> | ||
| <param name="sampling_file" type="data" format="csv" label="Sampling file" /> | ||
| <param name="sample_volume" type="integer" value="10000" min="1" max="1000000" label="Wanted sample volume in the destination plate" /> | ||
| <section name="adv" title="Advanced Options" expanded="false"> | ||
| <param name="start_well_src_plt" type="text" value="A1" label="Starting well for the source plate"> | ||
| <validator type="empty_field" message="Not empty"/> | ||
| <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator> | ||
| </param> | ||
| <param name="start_well_dst_plt" type="text" value="A1" label="Starting well for the destination plate"> | ||
| <validator type="empty_field" message="Not empty"/> | ||
| <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator> | ||
| </param> | ||
| <param name="plate_dims" type="text" value="16x24" label="Plate dimensions (Format: NxM)"> | ||
| <validator type="empty_field" message="Not empty"/> | ||
| <validator type="regex" message="An 'x' separator is expected">^(?:\d+x\d+)$</validator> | ||
| </param> | ||
| <param name="default_well_capacity" type="integer" value="60000" min="1" max="250000" label="Default well capacity in nL for components not specified in well_capacity" /> | ||
| <param name="default_dead_volume" type="integer" value="15000" min="1" max="250000" label="Default dead volume in nL for the source plate"/> | ||
| <param name="num_replicates" type="integer" value="1" min="1" max="10" label="Number of wanted replicates"/> | ||
| <repeat name="rep" title="Specific components"> | ||
| <param name="component_name" type="text" value="" label="Component Name"> | ||
| <validator type="empty_field" message="Not empty"/> | ||
| </param> | ||
| <param name="well_capacity" type="integer" value="60000" min="1" max="250000" label="Well capacity" /> | ||
| <param name="dead_volumes" type="integer" value="15000" min="1" max="250000" label="Dead volumes" /> | ||
| </repeat> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output_source_plate" format="csv" label="${tool.name} - Source" /> | ||
| <data name="output_destination_plate" format="csv" label="${tool.name} - Destination" /> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <!-- python -m icfree.plate_designer sampling.test-1.csv 6000 -default_well_capacity 60000 -default_dead_volume 20000 -num_replicates 1 --> | ||
| <param name="sampling_file" value="sampling.test-1.csv" /> | ||
| <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_designer.source_plate.test-1.csv" ftype="csv" compare="diff" /> | ||
| <output name="output_destination_plate" file="plates_designer.destination_plate.test-1.csv" ftype="csv" compare="diff" /> | ||
| </test> | ||
| <test> | ||
| <!-- python -m icfree.plate_designer sampling.test-1.csv '5000' -start_well_src_plt 'A1' -start_well_dst_plt 'A1' -plate_dims '16x24' -well_capacity 'Hela lysate=3000,Access prot 50X=4000,Reaction mix=3000,RNA 1ug/uL=2000' -default_well_capacity '60000' -dead_volumes 'Hela lysate=30,Access prot 50X=5,Reaction mix=10,RNA 1ug/uL=20' -default_dead_volume '20000' -num_replicates '2' --> | ||
| <param name="sampling_file" value="sampling.test-1.csv" /> | ||
| <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_designer.source_plate.test-2.csv" ftype="csv" compare="diff" /> | ||
| <output name="output_destination_plate" file="plates_designer.destination_plate.test-2.csv" ftype="csv" compare="diff" /> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Plates Generator | ||
| ================ | ||
| Prepare source and destination well-plate mappings with advanced options. | ||
| ]]></help> | ||
| <expand macro="creator"/> | ||
| <expand macro="citation"/> | ||
| </tool> |