Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
changeset 6:8dd4b25716d1 draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit 05004076adb510abc08f6c1e28ba22b2c1a29534
| author | sanbi-uwc |
|---|---|
| date | Sat, 05 Mar 2016 07:55:06 -0500 |
| parents | b7c01f1d6451 |
| children | d04a59b76845 |
| files | data_manager/novocraft_index_builder.py data_manager/novocraft_index_builder.xml data_manager_conf.xml tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/data_manager/novocraft_index_builder.py Sat Mar 05 07:05:30 2016 -0500 +++ b/data_manager/novocraft_index_builder.py Sat Mar 05 07:55:06 2016 -0500 @@ -14,7 +14,7 @@ from json import loads, dumps -DEFAULT_DATA_TABLE_NAME = "novocraft_indexes" +DEFAULT_DATA_TABLE_NAME = "novocraft_index" def get_dbkey_id_name(params, dbkey_description=None): dbkey = params['param_dict']['dbkey'] @@ -81,7 +81,7 @@ parser = argparse.ArgumentParser(description="Generate Novo-align genome index and JSON describing this") parser.add_argument('output_filename') parser.add_argument('--dbkey_description') - parser.add_argument('--data_table_name', default='novocraft_indexes') + parser.add_argument('--data_table_name', default='novocraft_index') args = parser.parse_args() filename = args.output_filename
--- a/data_manager/novocraft_index_builder.xml Sat Mar 05 07:05:30 2016 -0500 +++ b/data_manager/novocraft_index_builder.xml Sat Mar 05 07:55:06 2016 -0500 @@ -6,7 +6,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_indexes" + novocraft_index_builder.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() } --data_table_name "novocraft_index" </command> <inputs> <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
--- a/data_manager_conf.xml Sat Mar 05 07:05:30 2016 -0500 +++ b/data_manager_conf.xml Sat Mar 05 07:55:06 2016 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="utf-8" ?> <data_managers> <data_manager tool_file="data_manager/novocraft_index_builder.xml" id="novocraft_index_builder" version="0.0.1"> - <data_table name="novocraft_indexes"> + <data_table name="novocraft_index"> <output> <column name="value" /> <column name="dbkey" />
--- a/tool_data_table_conf.xml.sample Sat Mar 05 07:05:30 2016 -0500 +++ b/tool_data_table_conf.xml.sample Sat Mar 05 07:55:06 2016 -0500 @@ -1,5 +1,5 @@ <tables> - <table name="novocraft_indexes" comment_char="#"> + <table name="novocraft_index" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/novocraft_index.nix" /> </table>