diff data_manager/rna_star_index_builder.py @ 1:6127cd38980b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rna_star_index_builder.py	Mon Jun 24 11:36:07 2019 -0400
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument( '--config-file' )
+    parser.add_argument( '--value' )
+    parser.add_argument( '--dbkey' )
+    parser.add_argument( '--name' )
+    parser.add_argument( '--subdir' )
+    parser.add_argument( '--data-table' )
+    parser.add_argument( '--with-gene-model', action='store_true' )
+    parser.add_argument( '--index-version' )
+
+    args = parser.parse_args()
+
+    if args.dbkey in [ None, '', '?' ]:
+        raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( args.dbkey ) )
+
+    with_gene_model = "0"
+    if args.with_gene_model:
+        with_gene_model = "1"
+
+    data_manager_dict = {'data_tables': {args.data_table: [dict({"value": args.value, "dbkey": args.dbkey, "name": args.name, "path": args.subdir, "with_gene_model": with_gene_model, "version": args.index_version} )]}}
+    open( args.config_file, 'w' ).write( json.dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+    main()