Mercurial > repos > tduigou > icfree_instructor

annotate instructor.xml @ 12:337634672ac5 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 1568ac8d21ca92c2325ef661498ee7a4b622ae5e
author tduigou
date Tue, 21 Mar 2023 09:43:58 +0000
parents 401d55846cbf
children 6e84e7a070f5
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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 #set sps = [], sws = [], dps = [], dws = []
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10 #for $x in $plates_generator:
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11 #set $fname = str($x.element_identifier)
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12 ln -sfn '$x' '$fname' &&
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13 #if $fname.startswith('source') and $fname.endswith('json'):
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14 #silent sps.append($fname)
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15 #else if $fname.startswith('source') and $fname.endswith('tsv'):
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16 #silent sws.append($fname)
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17 #else if $fname.startswith('destination') and $fname.endswith('json'):
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18 #silent dps.append($fname)
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19 #else if $fname.startswith('destination') and $fname.endswith('tsv'):
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20 #silent dsws.append($fname)
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21 #end if
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22 #end for
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23 python -m icfree.instructor
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24 --source_plates '" "'.join($sps)
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25 --source_wells '" "'.join($sws)
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26 --dest_plates '" "'.join($dps)
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27 --dest_wells '" "'.join($dws)
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28 -spt '$source_plate'
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29 --robot '$robot'
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30 --output-folder '.' &&
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eac0d2bd8dd8 planemo upload for repository https://github.com/brsynth/icfree-ml commit 85914678915691d3ec8f0477f8bc7bcfa8518590
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31 mv instructions.csv '$output_instruction' &&
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32 #if not os.path.isfile('volume_warning.tsv')
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33 touch volume_warning.tsv &&
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34 #end if
eac0d2bd8dd8 planemo upload for repository https://github.com/brsynth/icfree-ml commit 85914678915691d3ec8f0477f8bc7bcfa8518590
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35 mv volume_warning.tsv '$output_warning'
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36 ]]></command>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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37 <inputs>
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38 <param name="plates_generator" type="data_collection" collection_type="list" format="json,tabular" label="Source/Destination corresponding to plate/wells" help="Output from iCFree plates generator"/>
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39 <param name="robot" type="select" label="Robot name">
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40 <option value="ECHO" selected="true">ECHO</option>
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41 </param>
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42 <param name="source_plate" type="select" label="Source plate type">
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43 <option value="384PP_AQ_GP3" selected="true">384PP_AQ_GP3</option>
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44 <option value="384_AQ_CP">384_AQ_CP</option>
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45 </param>
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46 </inputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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47 <outputs>
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48 <data name="output_warning" format="tsv" label="${tool.name} - Warning" />
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49 <data name="output_instruction" format="csv" label="${tool.name} - Instruction" />
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50 </outputs>
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51 <tests>
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52 <test>
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53 <!-- test 1: check if identical outputs are produced with default parameters -->
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54 <param name="plates_generator">
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55 <collection type="list">
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56 <element name="plates_generator_source_plate_1" value="plates_generator_source_plate_1.test-1.json" />
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57 <element name="plates_generator_source_plate_1.test-1.tsv" value="plates_generator_source_plate_1.test-1.tsv" />
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58 <element name="plates_generator_destination_plate_1.test-1.json" value="plates_generator_destination_plate_1.test-1.json" />
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59 <element name="plates_generator_destination_plate_1.test-1.tsv" value="plates_generator_destination_plate_1.test-1.tsv" />
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60 </collection>
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61 </param>
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62 <output name="output_warning" ftype="tabular">
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63 <assert_contents>
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64 <has_n_lines n="12"/>
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65 <has_line_matching expression="^Parameter\tMin\tMax\tPlate$"/>
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66 </assert_contents>
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67 </output>
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68 <output name="output_instruction" file="instructor_instructions.csv" ftype="csv" compare="diff" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 Instructor
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73 ==========
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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74
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75 The module generates a list of instructions to perform the experiment.
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76
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77 Input
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78 -----
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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79 Required:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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80 * **Source plates file**: description of the source plates (source well name, source well volume...) (JSON format)
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81 * **Destination plates file**: description of the destination plates (destination well name, destination well volume...) (JSON format)
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82
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83 Advanced options:
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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84 -----------------
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85 * **Robot name**: name of the robot to generate instructions for (default: "echo")
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86
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87 Output
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88 ------
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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89 * **instructions**: contains the instructions to perform the experiment
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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90 * **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
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91 ]]></help>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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92 <expand macro="creator"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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93 <expand macro="citation"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
tduigou
parents:
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94 </tool>