Mercurial > repos > ufz > omero_get_value

comparison omero_get_value.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 86428b102388
children
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2:ad8ca0f76aaf 3:6ae415d8821c
1 <tool id="omero_get_value" name="OMERO get Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> 1 <tool id="omero_get_value" name="OMERO get Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2 <description> with ezomero </description> 2 <description> with ezomero </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">3</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">omero</xref> 8 <xref type="bio.tools">omero</xref>
9 </xrefs> 9 </xrefs>
10 <expand macro="ezomero_requirements"/> 10 <expand macro="ezomero_requirements"/>
11 <required_files>
12 <include path="connect_omero.py" />
13 <include path="omero_get_value.py" />
14 </required_files>
11 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #if $test_username != ""
17 export OMERO_USER="$test_username" &&
18 export OMERO_PASSWORD="$test_password" &&
19 #end if
20
12 mkdir output; 21 mkdir output;
13 python '$__tool_directory__/omero_get_value.py' 22 python '$__tool_directory__/omero_get_value.py'
14 --credential-file '$credentials'
15 @HOST_PORT@ 23 @HOST_PORT@
16 --obj_type '$obj_type' 24 --obj_type '$obj_type'
17 #if $ids_input.ids_format == "values" 25 #if $ids_input.ids_format == "values"
18 --ids ${str($ids_input.ids).replace(',', ' ')} 26 --ids ${str($ids_input.ids).replace(',', ' ')}
19 #else 27 #else
20 --ids_path '$ids_input.ids_path' 28 --ids_path '$ids_input.ids_path'
21 #end if 29 #end if
30 @SESSION_ID@
22 --out_dir ./output/ 31 --out_dir ./output/
23 ]]></command> 32 ]]></command>
24 <configfiles>
25 <expand macro="credentials"/>
26 </configfiles>
27 <inputs> 33 <inputs>
28 <expand macro="host_port"/> 34 <expand macro="host_port"/>
29 <param argument="obj_type" type="select" optional="false" label="Type of object to fetch:"> 35 <param argument="obj_type" type="select" optional="false" label="Type of object to fetch:">
30 <option value="Annotation">Annotation</option> 36 <option value="Annotation">Annotation</option>
31 <option value="Tag">Tag</option> 37 <option value="Tag">Tag</option>