# HG changeset patch
# User richard-burhans
# Date 1720825203 0
# Node ID 168b0a92edd3e11a71fd0e278de0d7951cdf93c4
# Parent  ec709ce3d91bdbc01084cc53083ed32453da2372
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 53e28d4dd9ab352c94f91f952ac855b89197f032

diff -r ec709ce3d91b -r 168b0a92edd3 package_output.py
--- a/package_output.py	Thu Jul 11 15:50:48 2024 +0000
+++ b/package_output.py	Fri Jul 12 23:00:03 2024 +0000
@@ -270,8 +270,11 @@
 
 
 def main() -> None:
-    our_dirname: str = os.path.dirname(os.path.realpath(__file__))
-    lastz_command_config_file: str = os.path.join(our_dirname, "lastz-cmd.ini")
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--tool_directory", type=str, required=True, help="tool directory")
+    args = parser.parse_args()
+
+    lastz_command_config_file: str = os.path.join(args.tool_directory, "lastz-cmd.ini")
 
     config: configparser.ConfigParser = configparser.ConfigParser()
     config.read(lastz_command_config_file)
diff -r ec709ce3d91b -r 168b0a92edd3 segalign.xml
--- a/segalign.xml	Thu Jul 11 15:50:48 2024 +0000
+++ b/segalign.xml	Fri Jul 12 23:00:03 2024 +0000
@@ -173,7 +173,8 @@
 
 #if $segalign_mode == "segalign_diagonal_partition"
         &&
-        python '$__tool_directory__/package_output.py'
+        python '$__tool_directory__/package_output.py' \
+            --tool_directory '$__tool_directory__'
 #end if
 
     ]]></command>