Mercurial > repos > ufz > omero_get_value

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 3f4e79a4e8350481f3c8d70bc64f01b4cb0a4bf0
author ufz
date Fri, 13 Jun 2025 20:46:09 +0000
parents b3320a1f2120
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b3320a1f2120 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@">23.0</token>
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b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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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>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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10 <requirement type="package" version="2.2.2">pandas</requirement>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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11 <yield/>
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12 </requirements>
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13 </xml>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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15 <xml name="omeropy_requirements">
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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16 <requirements>
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17 <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
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18 <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
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19 <requirement type="package" version="21.0.2">openjdk</requirement>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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20 <yield/>
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21 </requirements>
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22 </xml>
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23
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b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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25 <xml name="host_port">
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26 <param name="omero_host" type="text" label="OMERO host URL">
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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27 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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28 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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29 </param>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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30 <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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31 <param name="test_username" type="hidden" value=""/>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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32 <param name="test_password" type="hidden" value=""/>
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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33 </xml>
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34 <token name="@HOST_PORT@">
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35 --host '$omero_host'
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36 --port $omero_port
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37 </token>
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38
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39 <xml name="credentials">
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40 <configfile name="credentials"><![CDATA[
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41 {
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42 "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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43 "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
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44 }
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45 ]]></configfile>
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46 </xml>
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47
b3320a1f2120 planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 54b50795912de3f2508cfcfc6911d71a94b34c56
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48 <token name="@SECURITY_DISCLAIMER@">
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49 **OMERO-suite Security Diclaimer:** To utilize the OMERO tools, the user must trust Galaxy instances.
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50 The configuration file, which contains your OMERO password and username, is stored in the job working directory.
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51 This directory only exists during the runtime of the job and should only be accessible by the system user that runs the job.
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52 However, please be aware that your username and password may be exposed to users with administrative rights.
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53 We are working on increasing the security of the OMERO suite
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54 </token>
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55
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56 </macros>