Mercurial > repos > dfornika > data_manager_mash_sketch_builder

changeset 21:b6c1d250bbe1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit 3a2663e8a2d8b056e041c3c9e550d8e522f44583-dirty"
author dfornika
date Mon, 24 Feb 2020 21:50:42 +0000
parents 2c596d4537c6
children
files data_manager/mash_sketch_builder.py data_manager/mash_sketch_builder.xml
diffstat 2 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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,
--- 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 @@
         <param type="text" name="sketch_name" label="Sketch name" />
         <param type="integer" name="sketch_size" value="1000" min="10" max="1000000" label="Sketch size" />
         <param type="integer" name="kmer_size" value="21" min="1" max="32" label="kmer size" />
+        <param type="float" name="probability_threshold" value="0.01" min="0." max="1." label="Probability threshold for warning about low k-mer size." />
         <param type="boolean" name="individual_sequences" truevalue="--individual-sequences" falsevalue="" label="Sketch individual sequences"/>
     </inputs>
     <outputs>