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comparison macros.xml @ 3:6ae415d8821c draft default tip

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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 15:04:30 +0000
parents b3320a1f2120
children
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2:ad8ca0f76aaf 3:6ae415d8821c
1 <macros> 1 <macros>
2 <!-- for historic reasons the omero-py version is used as the version for all tools --> 2 <!-- for historic reasons the omero-py version is used as the version for all tools -->
3 <token name="@TOOL_VERSION@">5.18.0</token> 3 <token name="@TOOL_VERSION@">5.18.0</token>
4 <token name="@EZOMERO_VERSION@">3.0.1</token> 4 <token name="@EZOMERO_VERSION@">3.0.1</token>
5 <token name="@PROFILE@">23.0</token> 5 <token name="@PROFILE@">25.1</token>
6 6
7 <xml name="ezomero_requirements"> 7 <xml name="ezomero_requirements">
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement> 9 <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement>
10 <requirement type="package" version="2.2.2">pandas</requirement> 10 <requirement type="package" version="2.2.2">pandas</requirement>
11 <yield/> 11 <yield/>
12 <expand macro="omero_credentials"/>
12 </requirements> 13 </requirements>
13 </xml> 14 </xml>
14 15
15 <xml name="omeropy_requirements"> 16 <xml name="omeropy_requirements">
16 <requirements> 17 <requirements>
17 <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement> 18 <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
18 <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 --> 19 <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
19 <requirement type="package" version="21.0.2">openjdk</requirement> 20 <requirement type="package" version="21.0.2">openjdk</requirement>
20 <yield/> 21 <yield/>
22 <expand macro="omero_credentials"/>
21 </requirements> 23 </requirements>
22 </xml> 24 </xml>
23 25
26 <xml name="omero_credentials">
27 <credentials name="OMERO" version="0.1" label="OMERO Credentials" description="Input a set of credentials to access a target OMERO.server">
28 <variable name="username" inject_as_env="OMERO_USER" optional="true" label="OMERO username" description="OMERO username" />
29 <secret name="password" inject_as_env="OMERO_PASSWORD" optional="true" label="OMERO password" description="OMERO password" />
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" />
31 </credentials>
32 </xml>
24 33
25 <xml name="host_port"> 34 <xml name="host_port">
26 <param name="omero_host" type="text" label="OMERO host URL"> 35 <param name="omero_host" type="text" label="OMERO host URL">
27 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator> 36 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
28 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator> 37 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
29 </param> 38 </param>
30 <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> 39 <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
31 <param name="test_username" type="hidden" value=""/> 40 <param name="test_username" type="hidden" value=""/>
32 <param name="test_password" type="hidden" value=""/> 41 <param name="test_password" type="hidden" value=""/>
42 <conditional name="session_id">
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)">
44 <option value="no">No</option>
45 <option value="yes">Yes</option>
46 </param>
47 <when value="yes">
48 <param name="close_connection" type="boolean" truevalue="True" falsevalue="False" label="Close the connection after executing the tool?"
49 help="If yes, the current OMERO connection will be closed after tools execution. UUID key cannot be used again in further tools."/>
50 </when>
51 <when value="no">
52 </when>
53 </conditional>
33 </xml> 54 </xml>
55
34 <token name="@HOST_PORT@"> 56 <token name="@HOST_PORT@">
35 --host '$omero_host' 57 --host '$omero_host'
36 --port $omero_port 58 --port $omero_port
37 </token> 59 </token>
38 60
39 <xml name="credentials"> 61 <token name="@SESSION_ID@">
40 <configfile name="credentials"><![CDATA[ 62 #if $session_id.session_id_input== "yes"
41 { 63 --session_close $close_connection
42 "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)", 64 #else
43 "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)" 65 --session_close "True"
44 } 66 #end if
45 ]]></configfile> 67 </token>
46 </xml> 68
47 69
48 <token name="@SECURITY_DISCLAIMER@"> 70 <token name="@SECURITY_DISCLAIMER@">
49 **OMERO-suite Security Diclaimer:** To utilize the OMERO tools, the user must trust Galaxy instances. 71 **OMERO-suite Security Notice**
50 The configuration file, which contains your OMERO password and username, is stored in the job working directory. 72
51 This directory only exists during the runtime of the job and should only be accessible by the system user that runs the job. 73 To use the OMERO tools, you must trust the Galaxy instance hosting your job.
52 However, please be aware that your username and password may be exposed to users with administrative rights. 74 Your OMERO username and password are stored in a temporary configuration file during job execution.
53 We are working on increasing the security of the OMERO suite 75
76 This file is accessible only to the system account running the job,
77 but may in principle be viewed by Galaxy administrators with elevated rights.
78
79 The file is removed after job completion and is not persistently stored.
80 **We recommend using service-specific or temporary OMERO credentials whenever possible.**
81
82 We are actively working to further improve security,
83 for example by enabling the UUID-key authentication.
84 The European Galaxy Server is operated in compliance with the EU General Data Protection Regulation (GDPR).
54 </token> 85 </token>
55 86
56 </macros> 87 </macros>