Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 15:e6d850bb9fb6 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit c78b1532031ee875ff51cb2a4c73f4577bd07839
| author | sanbi-uwc |
|---|---|
| date | Wed, 18 May 2016 08:28:36 -0400 |
| parents | 4caf3e2d10e8 |
| children | b62c2af675b4 |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/build_ctb_gene.py Wed May 18 04:49:51 2016 -0400 +++ b/build_ctb_gene.py Wed May 18 08:28:36 2016 -0400 @@ -55,6 +55,7 @@ def main(): parser = argparse.ArgumentParser(description="Tool used to extract data about genes using locus_tags") + parser.add_argument('--outputfile') parser.add_argument('--outputdir') parser.add_argument('--input_file') parser.add_argument('--mount_point')
--- a/build_ctb_gene.xml Wed May 18 04:49:51 2016 -0400 +++ b/build_ctb_gene.xml Wed May 18 08:28:36 2016 -0400 @@ -9,7 +9,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - build_ctb_gene.py --outputdir "${os.path.join($outputFile1.files_path,'neo4jdb')}" --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} > ${outputFile1} + build_ctb_gene.py --outputfile "${outputFile1}" --outputdir "${os.path.join($outputFile1.files_path,'neo4jdb')}" --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} > ${outputFile1} </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />