# HG changeset patch
# User dfornika
# Date 1582578668 0
# Node ID 9e119de8edf45c34e3b62148c907eb1aab1ccd39
# Parent c842c12e81d99c133f92564a14a9fffebd18d9ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 3a2663e8a2d8b056e041c3c9e550d8e522f44583-dirty"
diff -r c842c12e81d9 -r 9e119de8edf4 data_manager/mash_sketch_builder.py
--- a/data_manager/mash_sketch_builder.py Mon Feb 24 19:17:36 2020 +0000
+++ b/data_manager/mash_sketch_builder.py Mon Feb 24 21:11:08 2020 +0000
@@ -27,6 +27,9 @@
'-p', str(mash_sketch_args["threads"]),
str(mash_sketch_args["fasta"]),
]
+
+ if mash_sketch_args["individual_sequences"]:
+ args = args + ["-i"]
subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory)
@@ -50,6 +53,7 @@
parser.add_argument('data_manager_json')
parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length')
parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length')
+ parser.add_argument('--individual-sequences', dest='individual_sequences', type=boolean, action='store_true' help='Sketch individual sequences (for multi-fasta files)')
parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch')
parser.add_argument('--threads', dest='threads', default=1, help='threads')
parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch')
@@ -59,8 +63,6 @@
target_directory = data_manager_input['output_data'][0]['extra_files_path']
- pprint("***" + target_directory + "***" )
-
try:
os.mkdir( target_directory )
except OSError as exc:
@@ -75,6 +77,7 @@
"kmer_size": args.kmer_size,
"sketch_size": args.sketch_size,
"fasta": args.fasta,
+ "individual_sequences": args.individual_sequences,
"threads": args.threads,
}
diff -r c842c12e81d9 -r 9e119de8edf4 data_manager/mash_sketch_builder.xml
--- a/data_manager/mash_sketch_builder.xml Mon Feb 24 19:17:36 2020 +0000
+++ b/data_manager/mash_sketch_builder.xml Mon Feb 24 21:11:08 2020 +0000
@@ -18,6 +18,7 @@
--sketch-name '${sketch_name}'
--sketch-size '${sketch_size}'
--kmer-size '${kmer_size}'
+ ${individual_sequences}
]]>
@@ -40,6 +41,7 @@
+
@@ -51,8 +53,15 @@
-
-
+
10.1186/s13059-016-0997-x