Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 6:03ca4e5a3682 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 7fa283bb29cd154e974894b279265cf43881bccd
| author | sanbi-uwc |
|---|---|
| date | Mon, 16 May 2016 04:53:09 -0400 |
| parents | 6098213127d7 |
| children | d89a58d00a92 |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/build_ctb_gene.py Mon May 16 04:38:00 2016 -0400 +++ b/build_ctb_gene.py Mon May 16 04:53:09 2016 -0400 @@ -41,7 +41,7 @@ def main(): parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") parser.add_argument('output_file1') - parser.add_argument('output_dir') + parser.add_argument('--output_dir') parser.add_argument('--input_file') parser.add_argument('--mount_point') parser.add_argument('--username')
--- a/build_ctb_gene.xml Mon May 16 04:38:00 2016 -0400 +++ b/build_ctb_gene.xml Mon May 16 04:53:09 2016 -0400 @@ -10,7 +10,7 @@ </stdio> <command interpreter="python"> build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} \ - --username ${neo4j_db_username} --password ${neo4j_db_password} --url ${neo4j_db_url} --port ${neo4j_db_port} + --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />