Mercurial > repos > richard-burhans > segalign
changeset 11:168b0a92edd3 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 53e28d4dd9ab352c94f91f952ac855b89197f032
| author | richard-burhans |
|---|---|
| date | Fri, 12 Jul 2024 23:00:03 +0000 |
| parents | ec709ce3d91b |
| children | e6fde4082c76 |
| files | package_output.py segalign.xml |
| diffstat | 2 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- 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)
--- 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>