diff omero_roi_import.xml @ 3:dfe0aae1495c draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

--- a/omero_roi_import.xml	Thu Sep 12 16:30:36 2024 +0000
+++ b/omero_roi_import.xml	Tue Oct 22 11:53:15 2024 +0000
@@ -1,46 +1,28 @@
-<tool id="omero_roi_import" name="OMERO ROI Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
-      profile="20.01" license="MIT">
+<tool id="omero_roi_import" name="OMERO ROI Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description> with ezomero </description>
     <macros>
-        <token name="@TOOL_VERSION@">5.18.0</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">4</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">omero</xref>
     </xrefs>
-    <requirements>
-        <requirement type="package" version="3.0.1">ezomero</requirement>
-        <requirement type="package" version="2.2.2">pandas</requirement>
-        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
-        <requirement type="package" version="21.0.2">openjdk</requirement>
-    </requirements>
+    <expand macro="ezomero_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/omero_roi_upload.py'
         --input_file '$input'
         --image_id $id
         --credential-file '$credentials'
-        --host '$omero_host'
-        --port $omero_port
+        @HOST_PORT@
         --log_file '$log'
     ]]></command>
     <configfiles>
-        <configfile name="credentials"><![CDATA[
-{
-    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
-    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
-}
-        ]]></configfile>
+        <expand macro="credentials"/>
     </configfiles>
     <inputs>
+        <expand macro="host_port"/>
         <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/>
         <param argument="id" type="integer" value="" optional="false" label="Image ID where annotate the ROIs"/>
-        <param name="omero_host" type="text" label="OMERO host URL">
-            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
-            <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
-        </param>
-        <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
-        <param name="test_username" type="hidden" value=""/>
-        <param name="test_password" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="log" format="txt"/>