diff rename_tiff_channels.xml @ 6:4763362914f4 draft default tip

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5c324d06ad54dca76aa2b4c8118df5654f49da66

--- a/rename_tiff_channels.xml	Thu Jul 11 22:41:10 2024 +0000
+++ b/rename_tiff_channels.xml	Mon Jul 15 21:37:39 2024 +0000
@@ -59,7 +59,7 @@
 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
 
 original_ome_xml = tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'))
-working_ome = ome_types.from_xml(original_ome_xml, parser = 'lxml')
+working_ome = ome_types.from_xml(original_ome_xml)
 
 for l_idx, level in enumerate(working_ome.images):
 
@@ -73,7 +73,7 @@
 
             print(f"Channel {c_idx} renamed to {new_name}")
 
-updated_ome_xml = working_ome.to_xml()
+updated_ome_xml = working_ome.to_xml().encode()
 tiffcomment(os.path.join(cwd, 'renamed_image.ome.tiff'), updated_ome_xml)
 
 print("Updated OME-TIFF metadata:")
@@ -93,12 +93,13 @@
             <param name="channel_csv" value="rename_channels.csv" />
             <output name="renamed_image" ftype="ome.tiff">
                 <assert_contents>
-                    <has_size value="899000" delta="50000" />
+                    <has_size value="900000" delta="50000" />
                 </assert_contents>
             </output>
             <assert_stdout>
-                <has_text text="Channel 0 renamed to DNA_6" />
+                <has_text text="Channel 0 renamed to Hematoxylin" />
                 <has_text text="Updated OME-TIFF metadata" />
+                <has_text text="µm" />
             </assert_stdout>
         </test>
     </tests>