Mercurial > repos > ufz > omero_filter
annotate macros.xml @ 1:375281d11535 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
author | ufz |
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date | Tue, 29 Oct 2024 06:59:59 +0000 |
parents | 8a3324018fc5 |
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8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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1 <macros> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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2 <!-- for historic reasons the omero-py version is used as the version for all tools --> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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3 <token name="@TOOL_VERSION@">5.18.0</token> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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4 <token name="@EZOMERO_VERSION@">3.0.1</token> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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5 <token name="@PROFILE@">23.0</token> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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6 |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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7 <xml name="ezomero_requirements"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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8 <requirements> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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9 <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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10 <requirement type="package" version="2.2.2">pandas</requirement> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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11 <yield/> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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12 </requirements> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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13 </xml> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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14 |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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15 <xml name="omeropy_requirements"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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16 <requirements> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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17 <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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18 <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 --> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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19 <requirement type="package" version="21.0.2">openjdk</requirement> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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20 <yield/> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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21 </requirements> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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22 </xml> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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23 |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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24 |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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25 <xml name="host_port"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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26 <param name="omero_host" type="text" label="OMERO host URL"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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27 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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28 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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29 </param> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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30 <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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31 <param name="test_username" type="hidden" value=""/> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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32 <param name="test_password" type="hidden" value=""/> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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33 </xml> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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34 <token name="@HOST_PORT@"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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35 --host '$omero_host' |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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36 --port $omero_port |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
parents:
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37 </token> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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38 |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
ufz
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39 <xml name="credentials"> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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40 <configfile name="credentials"><![CDATA[ |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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41 { |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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42 "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)", |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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43 "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)" |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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44 } |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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45 ]]></configfile> |
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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46 </xml> |
1
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
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47 |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
ufz
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48 <token name="@SECURITY_DISCLAIMER@"> |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
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49 **OMERO-suite Security Diclaimer:** To utilize the OMERO tools, the user must trust Galaxy instances. |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
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50 The configuration file, which contains your OMERO password and username, is stored in the job working directory. |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
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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. |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
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52 However, please be aware that your username and password may be exposed to users with administrative rights. |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
ufz
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53 We are working on increasing the security of the OMERO suite |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
ufz
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54 </token> |
375281d11535
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b
ufz
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55 |
0
8a3324018fc5
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
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56 </macros> |