# HG changeset patch
# User dfornika
# Date 1582581042 0
# Node ID b6c1d250bbe1eb1f4ce2ca8be4502499ce0f07cf
# Parent 2c596d4537c6dd729eae4cf92e90a9941ef55bd9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 3a2663e8a2d8b056e041c3c9e550d8e522f44583-dirty"
diff -r 2c596d4537c6 -r b6c1d250bbe1 data_manager/mash_sketch_builder.py
--- a/data_manager/mash_sketch_builder.py Mon Feb 24 21:33:01 2020 +0000
+++ b/data_manager/mash_sketch_builder.py Mon Feb 24 21:50:42 2020 +0000
@@ -8,7 +8,6 @@
import sys
import uuid
-from pprint import pprint
DATA_TABLE_NAME = "mash_sketches"
@@ -23,6 +22,7 @@
args = [
'-k', str(mash_sketch_args["kmer_size"]),
'-s', str(mash_sketch_args["sketch_size"]),
+ '-w', str(mash_sketch_args["probability_threshold"]),
'-o', str(sketch_path),
'-p', str(mash_sketch_args["threads"]),
str(mash_sketch_args["fasta"]),
@@ -53,6 +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('--probability-threshold', dest='probability_threshold', type=float, default=0.01, help='Probability threshold for warning about low k-mer size')
parser.add_argument('--individual-sequences', dest='individual_sequences', action='store_true', default=False, 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')
@@ -76,6 +77,7 @@
mash_sketch_args = {
"kmer_size": args.kmer_size,
"sketch_size": args.sketch_size,
+ "probability_threshold": args.probability_threshold,
"fasta": args.fasta,
"individual_sequences": args.individual_sequences,
"threads": args.threads,
diff -r 2c596d4537c6 -r b6c1d250bbe1 data_manager/mash_sketch_builder.xml
--- a/data_manager/mash_sketch_builder.xml Mon Feb 24 21:33:01 2020 +0000
+++ b/data_manager/mash_sketch_builder.xml Mon Feb 24 21:50:42 2020 +0000
@@ -18,6 +18,7 @@
--sketch-name '${sketch_name}'
--sketch-size '${sketch_size}'
--kmer-size '${kmer_size}'
+ --probability-threshold '${probability_threshold}'
${individual_sequences}
]]>
@@ -41,6 +42,7 @@
+