Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference
changeset 4:094bd0114876 draft
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 06f9376308b504cd2ab7a4ff0126ae70d73faacc
| author | sanbi-uwc |
|---|---|
| date | Thu, 13 Sep 2018 14:35:09 -0400 |
| parents | 203133a92000 |
| children | f0c7cab2f547 |
| files | data_manager/shapeit_ref.py data_manager/shapeit_ref.xml data_manager_conf.xml test-data/sample.out tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager/shapeit_ref.py Thu Sep 13 10:03:16 2018 -0400 +++ b/data_manager/shapeit_ref.py Thu Sep 13 14:35:09 2018 -0400 @@ -33,7 +33,7 @@ if __name__ == '__main__': parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data') parser.add_argument('key', help='Short key to identify this reference set (no spaces)') - parser.add_argument('description', help='Description of reference set') + parser.add_argument('name', help='Description of reference set') parser.add_argument('path', help='Filesystem path to directory containing this reference set') parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files') parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set') @@ -46,13 +46,13 @@ assert_prefix_exists(args.reference_prefix, args.path, 'reference') assert_prefix_exists(args.map_prefix, args.path, 'map') - for column in ('key', 'description', 'path', 'reference_prefix', 'map_prefix'): + for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'): value = getattr(args, column) if '\t' in value: exit("TAB character found in {} argument".format(column)) data_manager_dict = {} - data_table_entry = dict(value=args.key, description=args.description, path=args.path, + data_table_entry = dict(value=args.key, name=args.name, path=args.path, reference_prefix=args.reference_prefix, map_prefix=args.map_prefix) _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)
--- a/data_manager/shapeit_ref.xml Thu Sep 13 10:03:16 2018 -0400 +++ b/data_manager/shapeit_ref.xml Thu Sep 13 14:35:09 2018 -0400 @@ -1,8 +1,8 @@ -<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.4"> +<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.5"> <command detect_errors="aggressive"><![CDATA[ python $__tool_directory__/shapeit_ref.py '${value}' - '${description}' + '${name}' '${path}' '${reference_prefix}' '${map_prefix}' @@ -10,7 +10,7 @@ ]]></command>> <inputs> <param name="value" type="text" label="Short key to identify this reference set (no spaces)" /> - <param name="description" type="text" label="Description of the reference data" /> + <param name="name" type="text" label="Description of the reference data" /> <param name="path" type="text" label="Filesystem path to directory containing this reference set" /> <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" /> <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
--- a/data_manager_conf.xml Thu Sep 13 10:03:16 2018 -0400 +++ b/data_manager_conf.xml Thu Sep 13 14:35:09 2018 -0400 @@ -4,7 +4,7 @@ <data_table name="shapeit_ref"> <output> <column name="value" /> - <column name="description" /> + <column name="name" /> <column name="path" /> <column name="reference_prefix" /> <column name="map_prefix" />
--- a/test-data/sample.out Thu Sep 13 10:03:16 2018 -0400 +++ b/test-data/sample.out Thu Sep 13 14:35:09 2018 -0400 @@ -1,1 +1,1 @@ -{"data_tables": {"shapeit_ref": [{"description": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}} +{"data_tables": {"shapeit_ref": [{"name": "1000 Genomes Project (phase 3) haplotypes (http://mathgen.stats.ox.ac.uk/impute/1000GPX20Phase3.html)", "value": "1000GP_Phase3", "map_prefix": "genetic_map_", "path": "/tools/databases/1000G/1000GP_Phase3", "reference_prefix": "1000GP_Phase3_"}]}}
--- a/tool_data_table_conf.xml.sample Thu Sep 13 10:03:16 2018 -0400 +++ b/tool_data_table_conf.xml.sample Thu Sep 13 14:35:09 2018 -0400 @@ -1,6 +1,6 @@ <tables> <table name="shapeit_ref" comment_char="#"> - <columns>value, description, path, reference_prefix, map_prefix</columns> + <columns>value, name, path, reference_prefix, map_prefix</columns> <file path="tool-data/shapeit_ref.loc" /> </table> </tables> \ No newline at end of file