Mercurial > repos > ufz > omero_filter

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 233f0e70cb20a02ec8530dbcfd5c7e70eef74476
author ufz
date Mon, 26 Jan 2026 15:03:40 +0000
parents 063ce7148f7d
children
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063ce7148f7d planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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1 <macros>
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2 <!-- for historic reasons the omero-py version is used as the version for all tools -->
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3 <token name="@TOOL_VERSION@">5.18.0</token>
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4 <token name="@EZOMERO_VERSION@">3.0.1</token>
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5 <token name="@PROFILE@">25.1</token>
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7 <xml name="ezomero_requirements">
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8 <requirements>
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9 <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement>
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10 <requirement type="package" version="2.2.2">pandas</requirement>
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11 <yield/>
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12 <expand macro="omero_credentials"/>
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13 </requirements>
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14 </xml>
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16 <xml name="omeropy_requirements">
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17 <requirements>
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18 <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
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19 <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
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20 <requirement type="package" version="21.0.2">openjdk</requirement>
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21 <yield/>
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22 <expand macro="omero_credentials"/>
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23 </requirements>
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24 </xml>
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26 <xml name="omero_credentials">
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27 <credentials name="OMERO" version="0.1" label="OMERO Credentials" description="Input a set of credentials to access a target OMERO.server">
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28 <variable name="username" inject_as_env="OMERO_USER" optional="true" label="OMERO username" description="OMERO username" />
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29 <secret name="password" inject_as_env="OMERO_PASSWORD" optional="true" label="OMERO password" description="OMERO password" />
25d2036b9b8b planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 233f0e70cb20a02ec8530dbcfd5c7e70eef74476
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30 <secret name="uuid-key" inject_as_env="UUID_SESSION_KEY" optional="true" label="OMERO UUID Session Key" description="Input your session key here to connect using an existing OMERO session key. More information on how to find a session key: https://omero.readthedocs.io/en/stable/users/cli/sessions.html" />
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31 </credentials>
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32 </xml>
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34 <xml name="host_port">
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35 <param name="omero_host" type="text" label="OMERO host URL">
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36 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
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37 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
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38 </param>
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39 <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
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40 <param name="test_username" type="hidden" value=""/>
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41 <param name="test_password" type="hidden" value=""/>
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42 <conditional name="session_id">
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43 <param name="session_id_input" type="select" label="Create an OMERO session using a UUID key?" help="Connect to OMERO trough an existing connection (no password/username input)">
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44 <option value="no">No</option>
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45 <option value="yes">Yes</option>
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46 </param>
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47 <when value="yes">
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48 <param name="close_connection" type="boolean" truevalue="True" falsevalue="False" label="Close the connection after executing the tool?"
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49 help="If yes, the current OMERO connection will be closed after tools execution. UUID key cannot be used again in further tools."/>
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50 </when>
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51 <when value="no">
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52 </when>
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53 </conditional>
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54 </xml>
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55
0
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56 <token name="@HOST_PORT@">
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57 --host '$omero_host'
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58 --port $omero_port
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59 </token>
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60
4
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61 <token name="@SESSION_ID@">
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62 #if $session_id.session_id_input== "yes"
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63 --session_close $close_connection
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64 #else
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65 --session_close "True"
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66 #end if
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67 </token>
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68
0
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69
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70 <token name="@SECURITY_DISCLAIMER@">
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71 **OMERO-suite Security Notice**
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72
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73 To use the OMERO tools, you must trust the Galaxy instance hosting your job.
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74 Your OMERO username and password are stored in a temporary configuration file during job execution.
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75
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76 This file is accessible only to the system account running the job,
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77 but may in principle be viewed by Galaxy administrators with elevated rights.
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78
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79 The file is removed after job completion and is not persistently stored.
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80 **We recommend using service-specific or temporary OMERO credentials whenever possible.**
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81
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82 We are actively working to further improve security,
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83 for example by enabling the UUID-key authentication.
25d2036b9b8b planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 233f0e70cb20a02ec8530dbcfd5c7e70eef74476
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84 The European Galaxy Server is operated in compliance with the EU General Data Protection Regulation (GDPR).
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063ce7148f7d planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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85 </token>
063ce7148f7d planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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86
063ce7148f7d planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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87 </macros>