annotate plates_designer.xml @ 1:b3c862e8497f draft

planemo upload for repository https://github.com/brsynth/icfree-ml commit 96a30e92eab3144b924fdba7b63be10b218160a7-dirty
author tduigou
date Thu, 05 Sep 2024 07:07:03 +0000
parents 92adc3382124
children 5d3a54198bf9
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b3c862e8497f planemo upload for repository https://github.com/brsynth/icfree-ml commit 96a30e92eab3144b924fdba7b63be10b218160a7-dirty
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1 <tool id="icfree_plates_designer" name="iCFree plates designer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
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2 <description>Prepare source and destination well-plate mappings with advanced options.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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9 #set well_capacity = []
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10 #set dead_volumes = []
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11 #for $x in $adv.rep
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12 #silent well_capacity.append(str($x.component_name) + "=" + str($x.well_capacity))
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13 #silent dead_volumes.append(str($x.component_name) + "=" + str($x.dead_volumes))
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14 #end for
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15 #set swell_capacity = ','.join($well_capacity)
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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16 #set sdead_volumes = ','.join($dead_volumes)
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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17
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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18 python -m icfree.plate_designer
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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19 '$sampling_file'
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20 '$sample_volume'
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21 --start_well_src_plt '$adv.start_well_src_plt'
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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22 --start_well_dst_plt '$adv.start_well_dst_plt'
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23 --plate_dims '$adv.plate_dims'
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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24 #if len($well_capacity) > 0
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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25 --well_capacity '$swell_capacity'
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26 #end if
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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27 --default_well_capacity '$adv.default_well_capacity'
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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28 #if len($dead_volumes) > 0
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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29 --dead_volumes '$sdead_volumes'
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30 #end if
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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31 --default_dead_volume '$adv.default_dead_volume'
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32 --num_replicates '$adv.num_replicates' &&
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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33 mv source_plate.csv '$output_source_plate' &&
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34 mv destination_plate.csv '$output_destination_plate'
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35 ]]></command>
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36 <inputs>
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37 <param name="sampling_file" type="data" format="csv" label="Sampling file" />
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b3c862e8497f planemo upload for repository https://github.com/brsynth/icfree-ml commit 96a30e92eab3144b924fdba7b63be10b218160a7-dirty
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38 <param name="sample_volume" type="integer" value="10000" min="1" max="1000000" label="Wanted sample volume in the destination plate" />
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39 <section name="adv" title="Advanced Options" expanded="false">
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40 <param name="start_well_src_plt" type="text" value="A1" label="Starting well for the source plate">
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41 <validator type="empty_field" message="Not empty"/>
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42 <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator>
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43 </param>
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44 <param name="start_well_dst_plt" type="text" value="A1" label="Starting well for the destination plate">
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45 <validator type="empty_field" message="Not empty"/>
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46 <validator type="regex" message="Some letters followed by a number">^(?:[A-K]{1}([1-9]|1[0-2]))$</validator>
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47 </param>
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48 <param name="plate_dims" type="text" value="16x24" label="Plate dimensions (Format: NxM)">
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49 <validator type="empty_field" message="Not empty"/>
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50 <validator type="regex" message="An 'x' separator is expected">^(?:\d+x\d+)$</validator>
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51 </param>
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52 <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" />
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53 <param name="default_dead_volume" type="integer" value="15000" min="1" max="250000" label="Default dead volume in nL for the source plate"/>
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54 <param name="num_replicates" type="integer" value="1" min="1" max="10" label="Number of wanted replicates"/>
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55 <repeat name="rep" title="Specific components">
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56 <param name="component_name" type="text" value="" label="Component Name">
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57 <validator type="empty_field" message="Not empty"/>
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58 </param>
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59 <param name="well_capacity" type="integer" value="60000" min="1" max="250000" label="Well capacity" />
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60 <param name="dead_volumes" type="integer" value="15000" min="1" max="250000" label="Dead volumes" />
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61 </repeat>
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62 </section>
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63 </inputs>
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64 <outputs>
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65 <data name="output_source_plate" format="csv" label="${tool.name} - Source" />
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66 <data name="output_destination_plate" format="csv" label="${tool.name} - Destination" />
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67 </outputs>
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68 <tests>
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69 <test>
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70 <!-- python -m icfree.plate_designer sampling.test-1.csv 6000 -default_well_capacity 60000 -default_dead_volume 20000 -num_replicates 1 -->
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71 <param name="sampling_file" value="sampling.test-1.csv" />
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72 <param name="sample_volume" value="6000" />
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73 <param name="default_well_capacity" value="60000" />
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74 <param name="default_dead_volume" value="20000" />
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75 <param name="num_replicates" value="1" />
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76 <output name="output_source_plate" file="plates_designer.source_plate.test-1.csv" ftype="csv" compare="diff" />
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77 <output name="output_destination_plate" file="plates_designer.destination_plate.test-1.csv" ftype="csv" compare="diff" />
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78 </test>
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79 <test>
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80 <!-- 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' -->
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81 <param name="sampling_file" value="sampling.test-1.csv" />
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82 <param name="sample_volume" value="5000" />
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83 <param name="default_well_capacity" value="60000" />
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84 <param name="default_dead_volume" value="20000" />
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85 <param name="num_replicates" value="2" />
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86 <repeat name="rep">
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87 <param name="component_name" value="Hela lysate" />
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88 <param name="well_capacity" value="3000" />
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89 <param name="dead_volumes" value="30" />
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90 </repeat>
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91 <repeat name="rep">
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92 <param name="component_name" value="Access prot 50%" />
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93 <param name="well_capacity" value="4000" />
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94 <param name="dead_volumes" value="5" />
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95 </repeat>
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96 <repeat name="rep">
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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97 <param name="component_name" value="Reaction mix" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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98 <param name="well_capacity" value="3000" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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99 <param name="dead_volumes" value="10" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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100 </repeat>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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101 <repeat name="rep">
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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102 <param name="component_name" value="RNA 1ug/uL" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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103 <param name="well_capacity" value="2000" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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104 <param name="dead_volumes" value="20" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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105 </repeat>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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106 <output name="output_source_plate" file="plates_designer.source_plate.test-2.csv" ftype="csv" compare="diff" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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107 <output name="output_destination_plate" file="plates_designer.destination_plate.test-2.csv" ftype="csv" compare="diff" />
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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108 </test>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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109 </tests>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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110 <help><![CDATA[
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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111 Plates Generator
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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112 ================
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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113
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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114 Prepare source and destination well-plate mappings with advanced options.
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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115 ]]></help>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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116 <expand macro="creator"/>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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117 <expand macro="citation"/>
92adc3382124 planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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118 </tool>