# HG changeset patch
# User iuc
# Date 1491344036 14400
# Node ID 1f54e98616af3dc805cc0a1e309fc5cbe2af788b
# Parent 2a1ac1abc3f75cf9b9d5e04468cfe556c09fe7b5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
diff -r 2a1ac1abc3f7 -r 1f54e98616af data_manager/data_manager_sam_fasta_index_builder.py
--- a/data_manager/data_manager_sam_fasta_index_builder.py Wed Aug 26 13:22:37 2015 -0400
+++ b/data_manager/data_manager_sam_fasta_index_builder.py Tue Apr 04 18:13:56 2017 -0400
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
import json
import optparse
@@ -12,12 +12,13 @@
DEFAULT_DATA_TABLE_NAME = "fasta_indexes"
+
def get_id_name( params, dbkey, fasta_description=None):
- #TODO: ensure sequence_id is unique and does not already appear in location file
+ # TODO: ensure sequence_id is unique and does not already appear in location file
sequence_id = params['param_dict']['sequence_id']
if not sequence_id:
sequence_id = dbkey
-
+
sequence_name = params['param_dict']['sequence_name']
if not sequence_name:
sequence_name = fasta_description
@@ -25,16 +26,17 @@
sequence_name = dbkey
return sequence_id, sequence_name
+
def build_sam_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=DEFAULT_DATA_TABLE_NAME ):
- #TODO: allow multiple FASTA input files
+ # TODO: allow multiple FASTA input files
assert os.path.exists( fasta_filename ), 'FASTA file "%s" is missing, cannot build samtools index.' % fasta_filename
fasta_base_name = os.path.split( fasta_filename )[-1]
sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
os.symlink( fasta_filename, sym_linked_fasta_filename )
-
+
args = [ 'samtools', 'faidx' ]
args.append( sym_linked_fasta_filename )
- tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-sam_fa_index_builder-stderr" )
+ tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-sam_fa_index_builder-stderr")
proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
return_code = proc.wait()
if return_code:
@@ -51,37 +53,40 @@
data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
_add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
return data_manager_dict
+
def main():
- #Parse Command Line
parser = optparse.OptionParser()
parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
(options, args) = parser.parse_args()
-
+
filename = args[0]
-
+
params = json.loads( open( filename ).read() )
target_directory = params[ 'output_data' ][0]['extra_files_path']
os.mkdir( target_directory )
data_manager_dict = {}
-
+
if options.fasta_dbkey in [ None, '', '?' ]:
raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) )
-
+
sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description )
-
- #build the index
+
+ # build the index
build_sam_index( data_manager_dict, options.fasta_filename, target_directory, options.fasta_dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME )
-
- #save info to json file
+
+ # save info to json file
open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
-
-if __name__ == "__main__": main()
+
+
+if __name__ == "__main__":
+ main()
diff -r 2a1ac1abc3f7 -r 1f54e98616af data_manager/data_manager_sam_fasta_index_builder.xml
--- a/data_manager/data_manager_sam_fasta_index_builder.xml Wed Aug 26 13:22:37 2015 -0400
+++ b/data_manager/data_manager_sam_fasta_index_builder.xml Tue Apr 04 18:13:56 2017 -0400
@@ -3,23 +3,28 @@
samtools
- data_manager_sam_fasta_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "fasta_indexes"
+
-
-
+
+
-
.. class:: infomark
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
-
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
diff -r 2a1ac1abc3f7 -r 1f54e98616af tool_dependencies.xml
--- a/tool_dependencies.xml Wed Aug 26 13:22:37 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-
-
-
-
-
-