# HG changeset patch
# User goeckslab
# Date 1749680330 0
# Node ID 75bbd1b0e7bb74deee29ea7119565bf3b6d875ae
# Parent  302ddf03402fb4f991a4edfeb7183a54da535f0d
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf

diff -r 302ddf03402f -r 75bbd1b0e7bb main_macros.xml
--- a/main_macros.xml	Tue Jul 30 18:21:02 2024 +0000
+++ b/main_macros.xml	Wed Jun 11 22:18:50 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.1.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">20.01</token>
 
     <xml name="scimap_requirements">
diff -r 302ddf03402f -r 75bbd1b0e7bb mcmicro_to_anndata.py
--- a/mcmicro_to_anndata.py	Tue Jul 30 18:21:02 2024 +0000
+++ b/mcmicro_to_anndata.py	Wed Jun 11 22:18:50 2025 +0000
@@ -20,13 +20,17 @@
     with open(inputs, 'r') as param_handler:
         params = json.load(param_handler)
 
-    image_path = params['image_path']
+    image_path = params['image_path']['source_path']
     drop_markers = params['drop_markers']
     if not drop_markers:
         drop_markers = None
     else:
         drop_markers = [x.strip() for x in drop_markers.split(',')]
     options = params['options']
+    if not options.get('custom_imageid'):
+        element_identifier = params['image_path']['element_identifier']
+        # Might be a list on unpatched versions of Galaxy, xref: https://github.com/galaxyproject/galaxy/pull/20438
+        options['custom_imageid'] = element_identifier if isinstance(element_identifier, str) else element_identifier[0]
     for k, v in options.items():
         if v == '':
             options[k] = None