diff omero_metadata_import.xml @ 3:eba4011643dd draft

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

--- a/omero_metadata_import.xml	Thu Sep 12 16:30:50 2024 +0000
+++ b/omero_metadata_import.xml	Tue Oct 22 11:52:32 2024 +0000
@@ -1,24 +1,17 @@
-<tool id="omero_metadata_import" name="OMERO Metadata Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
-      profile="20.01" license="MIT">
+<tool id="omero_metadata_import" name="OMERO Metadata 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@">2</token>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">3</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 $__tool_directory__/omero_metadata_upload.py
         --credential-file '$credentials'
-        --host $omero_host
-        --port $omero_port
+        @HOST_PORT@
         --obj_type $obj_type
         --ann_type $ann_type
         --ann_file $ann_file
@@ -29,19 +22,10 @@
         #end if
     ]]></command>
     <configfiles>
-        <configfile name="credentials"><![CDATA[
-{
-    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
-    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
-}
-        ]]></configfile>
+        <expand macro="credentials"/>
     </configfiles>
     <inputs>
-        <param name="omero_host" type="text" label="OMERO host URL">
-            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</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"/>
+        <expand macro="host_port"/>
         <param argument="obj_type" type="select" optional="true" label="Target Object Type">
             <option value="project">Project</option>
             <option value="screen">Screen</option>
@@ -64,8 +48,6 @@
         </param>
         <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
         <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
-        <param name="test_username" type="hidden" value=""/>
-        <param name="test_password" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="log" format="txt"/>