Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder
changeset 9:ccb7ce1ad9b3 draft
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit fbd0bba2d1b19756849695e02e17d86076ca74a1
| author | sanbi-uwc |
|---|---|
| date | Fri, 12 Feb 2016 03:30:43 -0500 |
| parents | 56686a746b91 |
| children | 61084615bb57 |
| files | data_manager/rnastar_index_builder.py data_manager/rnastar_index_builder.xml data_manager_conf.xml tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 6 insertions(+), 7 deletions(-) [+] |
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--- a/data_manager/rnastar_index_builder.py Thu Feb 11 06:56:21 2016 -0500 +++ b/data_manager/rnastar_index_builder.py Fri Feb 12 03:30:43 2016 -0500 @@ -56,12 +56,13 @@ parser.add_argument('--fasta_filename') parser.add_argument('--fasta_dbkey') parser.add_argument('--fasta_description', default=None) -parser.add_argument('--data_table_name', default='rnastar_index') +parser.add_argument('--data_table_name', default='rnastar_indexes') args = parser.parse_args() filename = args.output_filename params = load(open(filename, 'rb')) +print(params) output_directory = params[ 'output_data' ][0]['extra_files_path'] makedirs( output_directory ) data_manager_dict = {} @@ -70,6 +71,5 @@ (sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description) data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory) -#dt_tables = {args.data_table_name : [data_table_entry]} output_datatable_dict = dict(data_tables={args.data_table_name : [data_table_entry]}) -open( filename, 'wb' ).write( dumps( output_datatable_dict ) ) \ No newline at end of file +open( filename, 'wb' ).write( dumps( output_datatable_dict ) )
--- a/data_manager/rnastar_index_builder.xml Thu Feb 11 06:56:21 2016 -0500 +++ b/data_manager/rnastar_index_builder.xml Fri Feb 12 03:30:43 2016 -0500 @@ -4,7 +4,7 @@ <requirements> <requirement type="package" version="2.4.0d">rnastar</requirement> </requirements> - <command interpreter="python">rnastar_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_index"</command> + <command interpreter="python">rnastar_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_indexes"</command> <inputs> <param name="input1" type="select" label="Genome to index(FASTA format)"> <options from_data_table="all_fasta"/> @@ -22,7 +22,6 @@ <!--</conditional>--> </inputs> <outputs> - <!-- <data from_work_dir="tempstargenomedir" auto_format="false"></data>--> <data name="out_file" format="data_manager_json" /> </outputs> <help>Help!</help>
--- a/data_manager_conf.xml Thu Feb 11 06:56:21 2016 -0500 +++ b/data_manager_conf.xml Fri Feb 12 03:30:43 2016 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="utf-8" ?> <data_managers> <data_manager tool_file="data_manager/rnastar_index_builder.xml" id="rnastar_index_builder" version="0.0.1"> - <data_table name="rnastar_index"> + <data_table name="rnastar_indexes"> <output> <column name="value" /> <column name="dbkey" />
--- a/tool_data_table_conf.xml.sample Thu Feb 11 06:56:21 2016 -0500 +++ b/tool_data_table_conf.xml.sample Fri Feb 12 03:30:43 2016 -0500 @@ -1,5 +1,5 @@ <tables> - <table name="rnastar_index" comment_char="#"> + <table name="rnastar_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/rnastar_index.loc" /> </table>