diff omero_import.xml @ 4:d0c0f3c95368 draft

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

--- a/omero_import.xml	Thu Sep 12 16:30:43 2024 +0000
+++ b/omero_import.xml	Tue Oct 22 11:53:53 2024 +0000
@@ -1,17 +1,13 @@
-<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
     <description> with omero-py </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="@TOOL_VERSION@">omero-py</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="omeropy_requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         #import re
 
@@ -24,10 +20,9 @@
 
         source '$credentials' &&
         omero import folder -T Dataset:name:$dataset_name
-            -s $omero_host
+            -s '$omero_host'
             -p $omero_port
             -u "\$OMERO_USER"
-            -w "\$OMERO_PASSWORD"
         > $log &&
 
         omero logout
@@ -39,15 +34,9 @@
         ]]></configfile>
     </configfiles>
     <inputs>
+        <expand macro="host_port"/>
         <param name="folder" type="data" format="avi,bmp,btf,cif,csv,eps,fits,fli,gif,hdr,html,jp2,jpg,mov,mrc,ndpi,nhdr,nrrd,ome.tiff,par,pbm,pcx,pgm,png,ppm,psd,scn,sif,svs,tf2,tf8,tif,tif,tiff,top,txt,vms,wav,xml,zip" multiple="true" optional="false" label="Images to import into OMERO"/>
         <param name="dataset_name" type="text" optional="false" label="Target Dataset Name"/>
-        <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 name="omero_port" type="integer" value="4064" optional="false" label="OMERO port"/>
-        <param name="test_username" type="hidden" value=""/>
-        <param name="test_password" type="hidden" value=""/>
     </inputs>
     <outputs>
         <data name="log" format="txt"/>