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comparison omero_get_id.xml @ 0:c23735b45a4a draft

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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
author ufz
date Tue, 22 Oct 2024 11:53:30 +0000
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1 <tool id="omero_get_id" name="OMERO get IDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description> with ezomero </description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">omero</xref>
9 </xrefs>
10 <expand macro="ezomero_requirements"/>
11 <command detect_errors="exit_code"><![CDATA[
12 python '$__tool_directory__'/omero_get_id.py
13 --credential-file '$credentials'
14 @HOST_PORT@
15 --final_obj_type '$cond_obj_type.final_obj_type'
16 --parent_obj_type '$cond_obj_type.parent_obj_type'
17 --parent_id $cond_obj_type.parent_id
18 --tsv_file '$tsv'
19 ]]></command>
20 <configfiles>
21 <expand macro="credentials"/>
22 </configfiles>
23 <inputs>
24 <expand macro="host_port"/>
25 <conditional name="cond_obj_type">
26 <param argument="final_obj_type" type="select" optional="false" label="Type of object to fetch ID:">
27 <option value="Project">All Project IDs</option>
28 <option value="Dataset">Dataset IDs</option>
29 <option value="Image">Image IDs</option>
30 <option value="Annotation">Annotation IDs (key values)</option>
31 <option value="Tag">Tag IDs</option>
32 <option value="Roi">ROI IDs</option>
33 <option value="Table">Table IDs</option>
34 </param>
35 <when value="Project">
36 <param name="parent_obj_type" type="hidden" value="All"/>
37 <param name="parent_id" type="hidden" value="0"/>
38 </when>
39 <when value="Dataset">
40 <param name="parent_obj_type" type="select" label="Which datasets?">
41 <option value="All">All datasets</option>
42 <option value="Project">Only datasets from a Project</option>
43 </param>
44 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the project (leave 0 if you selected All)."/>
45 </when>
46 <when value="Image">
47 <param name="parent_obj_type" type="select" label="Which images?">
48 <option value="All">All images</option>
49 <option value="Project">Only images from a Project</option>
50 <option value="Dataset">Only images from a Dataset</option>
51 <option value="Plate">Only images from a Plate</option>
52 <option value="Well">Only images from a Well</option>
53 </param>
54 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the parent object above (leave 0 if you selected All)."/>
55 </when>
56 <when value="Annotation">
57 <param name="parent_obj_type" type="select" label="Of which type of object?">
58 <option value="Project">Annotations from a Project</option>
59 <option value="Dataset">Annotations from a Dataset</option>
60 <option value="Plate">Annotations from a Plate</option>
61 <option value="Well">Annotations from a Well</option>
62 <option value="Image">Annotations from an Image</option>
63 </param>
64 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
65 </when>
66 <when value="Tag">
67 <param name="parent_obj_type" type="select" label="Of which type of object?">
68 <option value="Project">Tags from a Project</option>
69 <option value="Dataset">Tags from a Dataset</option>
70 <option value="Plate">Tags from a Plate</option>
71 <option value="Well">Tags from a Well</option>
72 <option value="Image">Tags from an Image</option>
73 </param>
74 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
75 </when>
76 <when value="Roi">
77 <param name="parent_obj_type" type="hidden" value="Image"/>
78 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the image from which you want to get ROI IDs."/>
79 </when>
80 <when value="Table">
81 <param name="parent_obj_type" type="select" label="Of which type of object?">
82 <option value="Project">Table from a Project</option>
83 <option value="Dataset">Table from a Dataset</option>
84 <option value="Plate">Table from a Plate</option>
85 <option value="Well">Table from a Well</option>
86 <option value="Image">Table from an Image</option>
87 </param>
88 <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
89 </when>
90 </conditional>
91 </inputs>
92 <outputs>
93 <data name="tsv" format="tabular"/>
94 </outputs>
95 <tests>
96 <test>
97 <param name="omero_host" value="host.docker.internal"/>
98 <param name="omero_port" value="6064"/>
99 <conditional name="cond_obj_type">
100 <param name="final_obj_type" value="Project"/>
101 </conditional>
102 <param name="test_username" value="root"/>
103 <param name="test_password" value="omero"/>
104 <output name="tsv" value="output_ids_project.tsv" ftype="tabular">
105 <assert_contents>
106 <has_text text="1"/>
107 </assert_contents>
108 </output>
109 </test>
110 <test>
111 <param name="omero_host" value="host.docker.internal"/>
112 <param name="omero_port" value="6064"/>
113 <conditional name="cond_obj_type">
114 <param name="final_obj_type" value="Dataset"/>
115 <param name="parent_obj_type" value="Project"/>
116 <param name="parent_id" value="1"/>
117 </conditional>
118 <param name="test_username" value="root"/>
119 <param name="test_password" value="omero"/>
120 <output name="tsv" value="output_ids_dataset.tsv" ftype="tabular">
121 <assert_contents>
122 <has_text text="1"/>
123 </assert_contents>
124 </output>
125 </test>
126 <test>
127 <param name="omero_host" value="host.docker.internal"/>
128 <param name="omero_port" value="6064"/>
129 <conditional name="cond_obj_type">
130 <param name="final_obj_type" value="Image"/>
131 <param name="parent_obj_type" value="Dataset"/>
132 <param name="parent_id" value="1"/>
133 </conditional>
134 <param name="test_username" value="root"/>
135 <param name="test_password" value="omero"/>
136 <output name="tsv" value="output_ids_image.tsv" ftype="tabular">
137 <assert_contents>
138 <has_text text="1"/>
139 </assert_contents>
140 </output>
141 </test>
142 <test>
143 <param name="omero_host" value="host.docker.internal"/>
144 <param name="omero_port" value="6064"/>
145 <conditional name="cond_obj_type">
146 <param name="final_obj_type" value="Tag"/>
147 <param name="parent_obj_type" value="Image"/>
148 <param name="parent_id" value="1"/>
149 </conditional>
150 <param name="test_username" value="root"/>
151 <param name="test_password" value="omero"/>
152 <output name="tsv" ftype="tabular">
153 <assert_contents>
154 <has_text text="1"/>
155 </assert_contents>
156 </output>
157 </test>
158 </tests>
159 <help>
160 Description
161 -----------
162
163 Tool to fetch project, dataset, images, annotations, tags, table and ROIs IDs user defined OMERO.server.
164
165 Options:
166 Project -> Project IDs present in the OMERO.server
167 Dataset -> Dataset IDs present in a specific Project or in the server
168 Image -> Image IDs present in a specific Dataset or Project or Well or Plate or in the server
169 Annotation (Key-Value Pairs) -> Annotation IDs linked to an Image or Dataset or Project or Well or Plate
170 Tag -> Tag IDs linked to an Image or Dataset or Project or Well or Plate
171 ROI -> ROI IDs linked to an Image
172 Table -> Table linked to an Image or Dataset or Project or Well or Plate
173
174 </help>
175 <citations>
176 <citation type="doi">10.1038/nmeth.1896</citation>
177 </citations>
178 </tool>