Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 9:9cc174f0fb9f draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 2b6755be1c76f3e4209f9723e7f50f945939244f
| author | sanbi-uwc |
|---|---|
| date | Mon, 16 May 2016 05:45:10 -0400 |
| parents | 56555326a056 |
| children | cb322069c7bc |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/build_ctb_gene.py Mon May 16 05:32:38 2016 -0400 +++ b/build_ctb_gene.py Mon May 16 05:45:10 2016 -0400 @@ -12,7 +12,8 @@ def build_ctb_gene(output_file1, output_dir, input_file, mount_point): # cmdline_str = "build_ctb_gene goterms ${}".format(input_file) - cmdline_str = "echo goterms" + cmdline_str = "echo %s" % input_file + output_dir = mount_point build_ctb = False try: os.system(cmdline_str)
--- a/build_ctb_gene.xml Mon May 16 05:32:38 2016 -0400 +++ b/build_ctb_gene.xml Mon May 16 05:45:10 2016 -0400 @@ -9,8 +9,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --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 ${db_settings.neo4j_db_port} + build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --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} </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />