Mercurial > repos > dfornika > data_manager_build_mash_sketch

changeset 2:ea2cee927c04 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mash_sketch/ commit 423cf96266f6ac433052ff72edb1397502313010-dirty
author dfornika
date Thu, 25 Jul 2019 13:42:02 -0400
parents 7aea7633ec0b
children b8681a7aab8e
files data_manager/mash_build_sketch.py
diffstat 1 files changed, 8 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/mash_build_sketch.py	Thu Jul 25 13:32:46 2019 -0400
+++ b/data_manager/mash_build_sketch.py	Thu Jul 25 13:42:02 2019 -0400
@@ -26,27 +26,16 @@
 
     database_path = database_value
 
-    for input_seq in mash_args['input_seqs']:
-        mash_sketch_args_list = [
-            '-p', mash_args['threads'],
-            '-k', mash_args['kmer_size'],
-            '-s', mash_args['sketch_size'],
-            input_seq,
-        ]
+    mash_sketch_args_list = [
+        '-p', mash_args['threads'],
+        '-k', mash_args['kmer_size'],
+        '-s', mash_args['sketch_size'],
+        '-i', mash_args['input_seq'],
+        '-o', 'sketch',
+    ]
         
-        subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list,
-                              cwd=os.path.join(target_directory, database_path, 'tmp'))
-
-    mash_paste_args_list = [
-        'sketch',
-        'tmp/*.msh'
-    ]
-
-    subprocess.check_call(['mash', 'paste'] + mash_sketch_args_list,
+    subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list,
                           cwd=os.path.join(target_directory, database_path))
-
-    subprocess.check_call(['rm' '-r' 'tmp']
-                          cwd=os.path.join(target_directory, database_path)))
     
     bagit_args_list = [
         database_path,