Mercurial > repos > tduigou > icfree_instructor

annotate instructor.xml @ 7:6f8e7e811333 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 394ca2ac7adcf41f39deb35433fc81b33747041c
author tduigou
date Wed, 15 Mar 2023 10:26:46 +0000
parents df5b3f40c0b6
children c8bd090fa47f
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f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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1 <tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Generates a list of Echo-compatible instructions to prepare samples</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[
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9 mkdir json tsv &&
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10 #set sps = []
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11 #for $x in $source_plates:
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12 ln -sfn '$x' 'json/$x.element_identifier' &&
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13 #silent sps.append('json/' + str($x.element_identifier))
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14 #end for
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15 #set s_sps = '" "'.join(sps)
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16 #set sws = []
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17 #for $x in $source_wells:
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18 ln -sfn '$x' 'tsv/$x.element_identifier' &&
6f8e7e811333 planemo upload for repository https://github.com/brsynth/icfree-ml commit 394ca2ac7adcf41f39deb35433fc81b33747041c
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19 #silent sws.append('tsv/' + str($x.element_identifier))
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20 #end for
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21 #set s_sws = '" "'.join(sws)
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22 #set dps = []
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23 #for $x in $dest_plates:
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6f8e7e811333 planemo upload for repository https://github.com/brsynth/icfree-ml commit 394ca2ac7adcf41f39deb35433fc81b33747041c
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24 ln -sfn '$x' 'json/$x.element_identifier' &&
6f8e7e811333 planemo upload for repository https://github.com/brsynth/icfree-ml commit 394ca2ac7adcf41f39deb35433fc81b33747041c
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25 #silent dps.append('json/' + str($x.element_identifier))
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26 #end for
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27 #set s_dps = '" "'.join(dps)
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28 #set dws = []
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29 #for $x in $dest_wells:
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30 ln -sfn '$x' 'tsv/$x.element_identifier' &&
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31 #silent dws.append('tsv/' + str($x.element_identifier))
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32 #end for
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33 #set s_dws = '" "'.join(dws)
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34 python -m icfree.instructor
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35 --source_plates '$s_sps'
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36 --source_wells '$s_sws'
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37 --dest_plates '$s_dps'
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38 --dest_wells '$s_dws'
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39 --output-folder '.' &&
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40 mv volume_warning.tsv '$output_warning' &&
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41 mv instructions.csv '$output_instruction'
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42 ]]></command>
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43 <inputs>
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44 <param name="source_plates" type="data_collection" collection_type="list" format="json" label="Source plates information (json)" />
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45 <param name="source_wells" type="data_collection" collection_type="list" format="tabular" label="Source wells information (tsv)" />
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46 <param name="dest_plates" type="data_collection" collection_type="list" format="json" label="Destination plates information (json)" />
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47 <param name="dest_wells" type="data_collection" collection_type="list" format="tabular" label="Destination wells information (tsv)" />
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48 </inputs>
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49 <outputs>
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50 <data name="output_warning" format="tsv" label="${tool.name} - Warning" />
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51 <data name="output_instruction" format="csv" label="${tool.name} - Instruction" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <!-- test 1: check if identical outputs are produced with default parameters -->
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56 <param name="source_plates">
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57 <collection type="list">
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58 <element name="plates_generator_source_plate_1" value="plates_generator_source_plate_1.test-1.json" />
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59 </collection>
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60 </param>
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61 <param name="source_wells">
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62 <collection type="list">
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63 <element name="plates_generator_source_plate_1.test-1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
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64 </collection>
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65 </param>
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66 <param name="dest_plates">
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67 <collection type="list">
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68 <element name="plates_generator_destination_plate_1.test-1.json" value="plates_generator_destination_plate_1.test-1.json" />
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69 </collection>
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70 </param>
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71 <param name="dest_wells">
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72 <collection type="list">
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73 <element name="plates_generator_destination_plate_1.test-1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
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74 </collection>
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75 </param>
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76 <output name="output_warning" ftype="tabular">
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77 <assert_contents>
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78 <has_n_lines n="12"/>
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79 <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
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80 </assert_contents>
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81 </output>
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82 <output name="output_instruction" file="instructor_instructions.csv" ftype="csv" compare="diff" />
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 Instructor
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87 ==========
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88
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89 The module generates a list of instructions to perform the experiment.
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90
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91 Input
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92 -----
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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93 Required:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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94 * **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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95 * **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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96
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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97 Advanced options:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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98 -----------------
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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99 * **Robot name**: name of the robot to generate instructions for (default: "echo")
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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100
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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101 Output
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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102 ------
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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103 * **instructions**: contains the instructions to perform the experiment
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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104 * **volumes_warning**: contains the volumes that may cause issues with the chosen robot
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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105 ]]></help>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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106 <expand macro="creator"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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107 <expand macro="citation"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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108 </tool>