Mercurial > repos > yating-l > data_manager_fetch_reference_data
changeset 3:2804b5f00dc7 draft
planemo upload
| author | yating-l |
|---|---|
| date | Wed, 03 May 2017 16:52:09 -0400 |
| parents | c4737db26737 |
| children | 464d75111b16 |
| files | data_manager/fetch_reference_data.py data_manager/fetch_reference_data.xml |
| diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager/fetch_reference_data.py Wed May 03 16:32:05 2017 -0400 +++ b/data_manager/fetch_reference_data.py Wed May 03 16:52:09 2017 -0400 @@ -53,9 +53,10 @@ def main(): #Parse Command Line parser = argparse.ArgumentParser() + parser.add_argument('-o', '--out', help='Output file') args = parser.parse_args() - filename = args[0] + filename = args.out params = from_json_string(open(filename).read()) target_directory = params['output_data'][0]['extra_files_path']
--- a/data_manager/fetch_reference_data.xml Wed May 03 16:32:05 2017 -0400 +++ b/data_manager/fetch_reference_data.xml Wed May 03 16:52:09 2017 -0400 @@ -1,6 +1,6 @@ <tool id="data_manager_fetch_reference_data" name="Reference data for GlimmerHMM" version="0.0.1" tool_type="manage_data"> <description>fetching reference data for GlimmerHMM</description> - <command interpreter="python">fetch_reference_data.py "${out_file}"</command> + <command interpreter="python">fetch_reference_data.py -o "${out_file}"</command> <inputs> <param name="genome_id" type="text" label="Id of the reference genome" /> <param name="genome_name" type="text" label="Name of the reference genome" />