Mercurial > repos > tduigou > icfree_instructor

annotate instructor.xml @ 21:80516b9b1caa draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit b669b043a7cd633a9ba1ac2cf2a7f3ed09c3e92e
author tduigou
date Tue, 10 Sep 2024 08:17:10 +0000
parents ab9f4c430d8f
children 5ba334474596
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ab9f4c430d8f planemo upload for repository https://github.com/brsynth/icfree-ml commit 0cc2a71b09ae9b47c72b1a34c531a858335eb772
tduigou
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1 <tool id="icfree_instructor" name="iCFree instructor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT">
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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"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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7 <expand macro="stdio"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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8 <command detect_errors="exit_code"><![CDATA[
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9 python -m icfree.instructor
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10 '$source_plate_file'
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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11 '$destination_plate_file'
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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12 'instructor.csv'
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80516b9b1caa planemo upload for repository https://github.com/brsynth/icfree-ml commit b669b043a7cd633a9ba1ac2cf2a7f3ed09c3e92e
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13 --source_plate_type '$adv.source_plate_type'
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f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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14 --max_transfer_volume '$max_transfer_volume'
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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15 #if str($adv.split_threshold) != ''
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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16 --split_threshold '$split_threshold'
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337634672ac5 planemo upload for repository https://github.com/brsynth/icfree-ml commit 1568ac8d21ca92c2325ef661498ee7a4b622ae5e
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17 #end if
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f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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18 #if str($adv.split_components) != ''
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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19 --split_components '$split_components'
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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20 #end if
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21 ]]></command>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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22 <inputs>
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f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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parents: 18
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23 <param name="source_plate_file" type="data" format="csv" label="Source corresponding to plate/wells" help="Output from iCFree plates designer"/>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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24 <param name="destination_plate_file" type="data" format="csv" label="Destination corresponding to plate/wells" help="Output from iCFree plates designer"/>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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25 <section name="adv" title="Advanced Options" expanded="false">
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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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." >
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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27 <validator type="empty_field" message="Source plate type is required"/>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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28 </param>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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parents: 18
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29 <param argument="max_transfer_volume" type="integer" min="1" max="50000" value="500" label="Maximum transfer volume" help="Maximum volume for a single transfer. If not specified, no splitting will be performed." />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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30 <param argument="split_threshold" type="integer" min="1" max="50000" value="500" label="Split threshold" help="Volume threshold above which transfers need to be split. If not specified, no splitting will be performed." />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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31 <param name="split_components" type="text" optional="true" label="Split components" help="Comma-separated list of component names to create separate files for." >
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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parents: 18
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32 </param>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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parents: 18
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33 </section>
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34 </inputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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35 <outputs>
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36 <collection name="output_instructor" type="list" label="${tool.name} - Instructor">
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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37 <discover_datasets pattern="__designation_and_ext__" format="csv" directory="."/>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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38 </collection>
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f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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39 </outputs>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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40 <tests>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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41 <test>
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f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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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' -->
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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43 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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44 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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45 <output_collection name="output_instructor" type="list" count="1">
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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46 <element name="instructor" file="instructor.test-1.csv" ftype="csv" compare="diff" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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47 </output_collection>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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48 </test>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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49 <test>
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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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' -->
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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51 <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
parents: 18
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52 <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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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" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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parents: 18
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54 <param name="split_components" value="Hela lysate,Access prot 50%" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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55 <output_collection name="output_instructor" type="list" count="3">
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
tduigou
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56 <element name="instructor" file="instructor.test-2.csv" ftype="csv" compare="diff" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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57 <element name="instructor_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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58 <!--
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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59 <element name="instructor_Access prot 50X" file="instructor.access.test-2.csv" ftype="csv" compare="diff" />
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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60 -->
f5df51d88aac planemo upload for repository https://github.com/brsynth/icfree-ml commit 7640e2163acff6c925cba16188eaa4ce54639180
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61 </output_collection>
0
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62 </test>
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63 </tests>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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64 <help><![CDATA[
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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65 Instructor
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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66 ==========
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67 The module generates a list of instructions for handling the generated plates.
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f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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68
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69 ]]></help>
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f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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70 <expand macro="creator"/>
f60f2f6ec0cc planemo upload for repository https://github.com/brsynth/icfree-ml commit d87d4a4d7c894f2d884a71a2acc35f93bc5bbe4b
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71 <expand macro="citation"/>
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72 </tool>