# HG changeset patch
# User sanbi-uwc
# Date 1455265843 18000
# Node ID ccb7ce1ad9b39a088628b61a865d2c317d8b5ced
# Parent  56686a746b911c39dcfb47c3a26d72d94b3f43a3
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit fbd0bba2d1b19756849695e02e17d86076ca74a1

diff -r 56686a746b91 -r ccb7ce1ad9b3 data_manager/rnastar_index_builder.py
--- 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 ) )
diff -r 56686a746b91 -r ccb7ce1ad9b3 data_manager/rnastar_index_builder.xml
--- 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>
diff -r 56686a746b91 -r ccb7ce1ad9b3 data_manager_conf.xml
--- 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" />
diff -r 56686a746b91 -r ccb7ce1ad9b3 tool_data_table_conf.xml.sample
--- 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>